Introduction to RNA-seq
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
@@ -646,7 +646,7 @@Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/01-intro-to-rnaseq.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/01-intro-to-rnaseq.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/02-setup.html b/02-setup.html index 00a3cb19..bbe26cfb 100644 --- a/02-setup.html +++ b/02-setup.html @@ -279,7 +279,7 @@RStudio Project and Experimental Data
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
@@ -637,7 +637,7 @@Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/02-setup.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/02-setup.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/03-import-annotate.html b/03-import-annotate.html index 471f2154..63fdada3 100644 --- a/03-import-annotate.html +++ b/03-import-annotate.html @@ -282,7 +282,7 @@Importing and annotating quantified data into R
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
@@ -514,7 +514,7 @@Challenge: Discuss the following points with your neig
-
+
- In
counts, the rows are genes just like the rows in
rowranges. The columns in counts are the
@@ -632,7 +632,7 @@ Challenge
-
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R
@@ -1008,7 +1008,7 @@ Challenge
-
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R
@@ -1132,7 +1132,7 @@ Challenge: How to subset to mRNA genes
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R
@@ -1320,7 +1320,7 @@ OUTPUT<
[13] BiocGenerics_0.50.0 knitr_1.49
loaded via a namespace (and not attached):
- [1] Matrix_1.7-1 bit_4.5.0 jsonlite_1.8.9
+ [1] Matrix_1.7-1 bit_4.5.0.1 jsonlite_1.8.9
[4] compiler_4.4.2 BiocManager_1.30.25 renv_1.0.11
[7] crayon_1.5.3 blob_1.2.4 Biostrings_2.72.1
[10] png_0.1-8 fastmap_1.2.0 yaml_2.3.10
@@ -1328,7 +1328,7 @@ OUTPUT<
[16] S4Arrays_1.4.1 DelayedArray_0.30.1 GenomeInfoDbData_1.2.12
[19] DBI_1.2.3 rlang_1.1.4 KEGGREST_1.44.1
[22] cachem_1.1.0 xfun_0.49 bit64_4.5.2
-[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.8
+[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.9
[28] cli_3.6.3 zlibbioc_1.50.0 grid_4.4.2
[31] vctrs_0.6.5 evaluate_1.0.1 abind_1.4-8
[34] httr_1.4.7 pkgconfig_2.0.3 tools_4.4.2
@@ -1405,7 +1405,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/03-import-annotate.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/03-import-annotate.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/04-exploratory-qc.html b/04-exploratory-qc.html
index f7175e2a..499fcf65 100644
--- a/04-exploratory-qc.html
+++ b/04-exploratory-qc.html
@@ -283,7 +283,7 @@
Exploratory analysis and quality control
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -858,33 +858,32 @@ OUTPUT<
[7] mgcv_1.9-1 png_0.1-8 vctrs_0.6.5
[10] pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3
[13] fastmap_1.2.0 XVector_0.44.0 labeling_0.4.3
-[16] utf8_1.2.4 promises_1.3.2 shinyAce_0.4.3
-[19] UCSC.utils_1.0.0 preprocessCore_1.66.0 xfun_0.49
-[22] cachem_1.1.0 zlibbioc_1.50.0 jsonlite_1.8.9
-[25] listviewer_4.0.0 later_1.4.1 DelayedArray_0.30.1
-[28] BiocParallel_1.38.0 parallel_4.4.2 cluster_2.1.6
-[31] R6_2.5.1 bslib_0.8.0 limma_3.60.6
-[34] jquerylib_0.1.4 Rcpp_1.0.13-1 iterators_1.0.14
-[37] knitr_1.49 httpuv_1.6.15 Matrix_1.7-1
-[40] splines_4.4.2 igraph_2.1.1 tidyselect_1.2.1
-[43] abind_1.4-8 yaml_2.3.10 doParallel_1.0.17
-[46] codetools_0.2-20 affy_1.82.0 miniUI_0.1.1.1
-[49] lattice_0.22-6 tibble_3.2.1 shiny_1.9.1
-[52] withr_3.0.2 evaluate_1.0.1 circlize_0.4.16
-[55] pillar_1.9.0 affyio_1.74.0 BiocManager_1.30.25
-[58] renv_1.0.11 DT_0.33 foreach_1.5.2
-[61] shinyjs_2.1.0 generics_0.1.3 munsell_0.5.1
-[64] scales_1.3.0 xtable_1.8-4 glue_1.8.0
-[67] tools_4.4.2 colourpicker_1.3.0 locfit_1.5-9.10
-[70] colorspace_2.1-1 nlme_3.1-166 GenomeInfoDbData_1.2.12
-[73] vipor_0.4.7 cli_3.6.3 fansi_1.0.6
-[76] viridisLite_0.4.2 S4Arrays_1.4.1 dplyr_1.1.4
-[79] gtable_0.3.6 rintrojs_0.3.4 sass_0.4.9
-[82] digest_0.6.37 SparseArray_1.4.8 ggrepel_0.9.6
-[85] farver_2.1.2 rjson_0.2.23 htmlwidgets_1.6.4
-[88] htmltools_0.5.8.1 lifecycle_1.0.4 shinyWidgets_0.8.7
-[91] httr_1.4.7 GlobalOptions_0.1.2 statmod_1.5.0
-[94] mime_0.12
+[16] promises_1.3.2 shinyAce_0.4.3 UCSC.utils_1.0.0
+[19] preprocessCore_1.66.0 xfun_0.49 cachem_1.1.0
+[22] zlibbioc_1.50.0 jsonlite_1.8.9 listviewer_4.0.0
+[25] later_1.4.1 DelayedArray_0.30.1 BiocParallel_1.38.0
+[28] parallel_4.4.2 cluster_2.1.8 R6_2.5.1
+[31] bslib_0.8.0 limma_3.60.6 jquerylib_0.1.4
+[34] Rcpp_1.0.13-1 iterators_1.0.14 knitr_1.49
+[37] httpuv_1.6.15 Matrix_1.7-1 splines_4.4.2
+[40] igraph_2.1.2 tidyselect_1.2.1 abind_1.4-8
+[43] yaml_2.3.10 doParallel_1.0.17 codetools_0.2-20
+[46] affy_1.82.0 miniUI_0.1.1.1 lattice_0.22-6
+[49] tibble_3.2.1 shiny_1.10.0 withr_3.0.2
+[52] evaluate_1.0.1 circlize_0.4.16 pillar_1.10.0
+[55] affyio_1.74.0 BiocManager_1.30.25 renv_1.0.11
+[58] DT_0.33 foreach_1.5.2 shinyjs_2.1.0
+[61] generics_0.1.3 munsell_0.5.1 scales_1.3.0
+[64] xtable_1.8-4 glue_1.8.0 tools_4.4.2
+[67] colourpicker_1.3.0 locfit_1.5-9.10 colorspace_2.1-1
+[70] nlme_3.1-166 GenomeInfoDbData_1.2.12 vipor_0.4.7
+[73] cli_3.6.3 viridisLite_0.4.2 S4Arrays_1.4.1
+[76] dplyr_1.1.4 gtable_0.3.6 rintrojs_0.3.4
+[79] sass_0.4.9 digest_0.6.37 SparseArray_1.4.8
+[82] ggrepel_0.9.6 farver_2.1.2 rjson_0.2.23
+[85] htmlwidgets_1.6.4 htmltools_0.5.8.1 lifecycle_1.0.4
+[88] shinyWidgets_0.8.7 httr_1.4.7 GlobalOptions_0.1.2
+[91] statmod_1.5.0 mime_0.12
@@ -957,7 +956,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/04-exploratory-qc.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/04-exploratory-qc.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/05-differential-expression.html b/05-differential-expression.html
index 7f152fb0..c95f9d53 100644
--- a/05-differential-expression.html
+++ b/05-differential-expression.html
@@ -283,7 +283,7 @@
Differential expression analysis
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -1004,7 +1004,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/05-differential-expression.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/05-differential-expression.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/06-extra-design.html b/06-extra-design.html
index 9b93676c..31e5037c 100644
--- a/06-extra-design.html
+++ b/06-extra-design.html
@@ -285,7 +285,7 @@
Extra exploration of design matrices
- Last updated on 2024-12-03 |
+
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Edit this page
@@ -646,7 +646,7 @@ Challenge
-
+
R
@@ -732,7 +732,7 @@ Challenge
-
+
R
@@ -1979,7 +1979,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/06-extra-design.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/06-extra-design.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/07-gene-set-analysis.html b/07-gene-set-analysis.html
index 04844a20..c7e48425 100644
--- a/07-gene-set-analysis.html
+++ b/07-gene-set-analysis.html
@@ -279,7 +279,7 @@
Gene set enrichment analysis
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -834,9 +834,9 @@ ROUTPUT
Unit: microseconds
- expr min lq mean median uq max neval
- fisher 242.563 244.937 262.70772 247.967 251.9505 1406.496 100
- hyper 1.492 1.693 2.33685 2.555 2.8555 6.101 100
+ expr min lq mean median uq max neval
+ fisher 242.642 249.1445 271.24591 252.195 262.1435 1561.651 100
+ hyper 1.473 1.7080 2.53325 2.720 2.9710 8.786 100
It is very astonishing that phyper() is hundreds of
times faster than fisher.test(). Main reason is in
@@ -990,7 +990,7 @@
Challenge
-
+
R
@@ -1611,7 +1611,7 @@ OUTPUT<
OUTPUT
---> Expected input gene ID: 73884,382007,13214,226356,208188,66197
+--> Expected input gene ID: 60597,11517,17864,100039030,54486,69496
OUTPUT
@@ -1888,19 +1888,19 @@ OUTPUT<
mmu04913 Ovarian steroidogenesis - Mus musculus (house mouse)
mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse)
GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
-mmu00590 16/460 89/9818 0.1797753 3.837030 5.960759 3.104291e-06
-mmu00591 12/460 55/9818 0.2181818 4.656759 6.029243 6.756868e-06
-mmu00565 11/460 48/9818 0.2291667 4.891214 5.991495 9.914058e-06
-mmu00592 8/460 25/9818 0.3200000 6.829913 6.470696 1.166851e-05
-mmu04913 12/460 64/9818 0.1875000 4.001902 5.341607 3.445424e-05
-mmu04061 14/460 95/9818 0.1473684 3.145355 4.658408 1.259362e-04
+mmu00590 16/451 89/9569 0.1797753 3.814345 5.932220 3.338144e-06
+mmu00591 12/451 55/9569 0.2181818 4.629228 6.002927 7.161290e-06
+mmu00565 11/451 48/9569 0.2291667 4.862297 5.965873 1.046503e-05
+mmu00592 8/451 25/9569 0.3200000 6.789534 6.446107 1.217181e-05
+mmu04913 12/451 64/9569 0.1875000 3.978243 5.316467 3.643828e-05
+mmu04061 14/451 95/9569 0.1473684 3.126759 4.633002 1.337191e-04
p.adjust qvalue
-mmu00590 0.0009101439 0.0007860892
-mmu00591 0.0009101439 0.0007860892
-mmu00565 0.0009101439 0.0007860892
-mmu00592 0.0009101439 0.0007860892
-mmu04913 0.0021499443 0.0018569019
-mmu04061 0.0065486813 0.0056560810
+mmu00590 0.0009494012 0.0008231987
+mmu00591 0.0009494012 0.0008231987
+mmu00565 0.0009494012 0.0008231987
+mmu00592 0.0009494012 0.0008231987
+mmu04913 0.0022737489 0.0019715029
+mmu04061 0.0069533935 0.0060290895
geneID
mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687
mmu00591 18783/211429/329502/78390/242546/18781/18784/13113/622127/232889/237625/11687
@@ -2647,7 +2647,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/07-gene-set-analysis.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/07-gene-set-analysis.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/08-next-steps.html b/08-next-steps.html
index 3db185ab..8de922a1 100644
--- a/08-next-steps.html
+++ b/08-next-steps.html
@@ -277,7 +277,7 @@
Next steps
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -424,7 +424,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/08-next-steps.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/08-next-steps.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index acd53dca..8bc758e6 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -265,7 +265,7 @@
Contributor Code of Conduct
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -340,7 +340,7 @@ Contributor Code of Conduct
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/CODE_OF_CONDUCT.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/CODE_OF_CONDUCT.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/LICENSE.html b/LICENSE.html
index 5ed6a5e1..97896f52 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -265,7 +265,7 @@
Licenses
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -388,7 +388,7 @@ Licenses
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/LICENSE.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/LICENSE.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/aio.html b/aio.html
index b4085f05..46eb54f0 100644
--- a/aio.html
+++ b/aio.html
@@ -329,7 +329,7 @@
Content from Introduction to RNA-seq
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -667,7 +667,7 @@ Key Points
Content from RStudio Project and Experimental Data
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -1002,7 +1002,7 @@ Key Points
Content from Importing and annotating quantified data into R
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -1241,7 +1241,7 @@ Challenge: Discuss the following points with your neig
-
+
- In
counts, the rows are genes just like the rows in
@@ -1367,7 +1367,7 @@ Challenge
-
+
R
@@ -1745,7 +1745,7 @@ Challenge
-
+
R
@@ -1873,7 +1873,7 @@ Challenge: How to subset to mRNA genes
-
+
R
@@ -2070,7 +2070,7 @@ OUTPUT<
[13] BiocGenerics_0.50.0 knitr_1.49
loaded via a namespace (and not attached):
- [1] Matrix_1.7-1 bit_4.5.0 jsonlite_1.8.9
+ [1] Matrix_1.7-1 bit_4.5.0.1 jsonlite_1.8.9
[4] compiler_4.4.2 BiocManager_1.30.25 renv_1.0.11
[7] crayon_1.5.3 blob_1.2.4 Biostrings_2.72.1
[10] png_0.1-8 fastmap_1.2.0 yaml_2.3.10
@@ -2078,7 +2078,7 @@ OUTPUT<
[16] S4Arrays_1.4.1 DelayedArray_0.30.1 GenomeInfoDbData_1.2.12
[19] DBI_1.2.3 rlang_1.1.4 KEGGREST_1.44.1
[22] cachem_1.1.0 xfun_0.49 bit64_4.5.2
-[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.8
+[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.9
[28] cli_3.6.3 zlibbioc_1.50.0 grid_4.4.2
[31] vctrs_0.6.5 evaluate_1.0.1 abind_1.4-8
[34] httr_1.4.7 pkgconfig_2.0.3 tools_4.4.2
@@ -2105,7 +2105,7 @@ Key Points
Content from Exploratory analysis and quality control
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -2711,33 +2711,32 @@ OUTPUT<
[7] mgcv_1.9-1 png_0.1-8 vctrs_0.6.5
[10] pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3
[13] fastmap_1.2.0 XVector_0.44.0 labeling_0.4.3
-[16] utf8_1.2.4 promises_1.3.2 shinyAce_0.4.3
-[19] UCSC.utils_1.0.0 preprocessCore_1.66.0 xfun_0.49
-[22] cachem_1.1.0 zlibbioc_1.50.0 jsonlite_1.8.9
-[25] listviewer_4.0.0 later_1.4.1 DelayedArray_0.30.1
-[28] BiocParallel_1.38.0 parallel_4.4.2 cluster_2.1.6
-[31] R6_2.5.1 bslib_0.8.0 limma_3.60.6
-[34] jquerylib_0.1.4 Rcpp_1.0.13-1 iterators_1.0.14
-[37] knitr_1.49 httpuv_1.6.15 Matrix_1.7-1
-[40] splines_4.4.2 igraph_2.1.1 tidyselect_1.2.1
-[43] abind_1.4-8 yaml_2.3.10 doParallel_1.0.17
-[46] codetools_0.2-20 affy_1.82.0 miniUI_0.1.1.1
-[49] lattice_0.22-6 tibble_3.2.1 shiny_1.9.1
-[52] withr_3.0.2 evaluate_1.0.1 circlize_0.4.16
-[55] pillar_1.9.0 affyio_1.74.0 BiocManager_1.30.25
-[58] renv_1.0.11 DT_0.33 foreach_1.5.2
-[61] shinyjs_2.1.0 generics_0.1.3 munsell_0.5.1
-[64] scales_1.3.0 xtable_1.8-4 glue_1.8.0
-[67] tools_4.4.2 colourpicker_1.3.0 locfit_1.5-9.10
-[70] colorspace_2.1-1 nlme_3.1-166 GenomeInfoDbData_1.2.12
-[73] vipor_0.4.7 cli_3.6.3 fansi_1.0.6
-[76] viridisLite_0.4.2 S4Arrays_1.4.1 dplyr_1.1.4
-[79] gtable_0.3.6 rintrojs_0.3.4 sass_0.4.9
-[82] digest_0.6.37 SparseArray_1.4.8 ggrepel_0.9.6
-[85] farver_2.1.2 rjson_0.2.23 htmlwidgets_1.6.4
-[88] htmltools_0.5.8.1 lifecycle_1.0.4 shinyWidgets_0.8.7
-[91] httr_1.4.7 GlobalOptions_0.1.2 statmod_1.5.0
-[94] mime_0.12
+[16] promises_1.3.2 shinyAce_0.4.3 UCSC.utils_1.0.0
+[19] preprocessCore_1.66.0 xfun_0.49 cachem_1.1.0
+[22] zlibbioc_1.50.0 jsonlite_1.8.9 listviewer_4.0.0
+[25] later_1.4.1 DelayedArray_0.30.1 BiocParallel_1.38.0
+[28] parallel_4.4.2 cluster_2.1.8 R6_2.5.1
+[31] bslib_0.8.0 limma_3.60.6 jquerylib_0.1.4
+[34] Rcpp_1.0.13-1 iterators_1.0.14 knitr_1.49
+[37] httpuv_1.6.15 Matrix_1.7-1 splines_4.4.2
+[40] igraph_2.1.2 tidyselect_1.2.1 abind_1.4-8
+[43] yaml_2.3.10 doParallel_1.0.17 codetools_0.2-20
+[46] affy_1.82.0 miniUI_0.1.1.1 lattice_0.22-6
+[49] tibble_3.2.1 shiny_1.10.0 withr_3.0.2
+[52] evaluate_1.0.1 circlize_0.4.16 pillar_1.10.0
+[55] affyio_1.74.0 BiocManager_1.30.25 renv_1.0.11
+[58] DT_0.33 foreach_1.5.2 shinyjs_2.1.0
+[61] generics_0.1.3 munsell_0.5.1 scales_1.3.0
+[64] xtable_1.8-4 glue_1.8.0 tools_4.4.2
+[67] colourpicker_1.3.0 locfit_1.5-9.10 colorspace_2.1-1
+[70] nlme_3.1-166 GenomeInfoDbData_1.2.12 vipor_0.4.7
+[73] cli_3.6.3 viridisLite_0.4.2 S4Arrays_1.4.1
+[76] dplyr_1.1.4 gtable_0.3.6 rintrojs_0.3.4
+[79] sass_0.4.9 digest_0.6.37 SparseArray_1.4.8
+[82] ggrepel_0.9.6 farver_2.1.2 rjson_0.2.23
+[85] htmlwidgets_1.6.4 htmltools_0.5.8.1 lifecycle_1.0.4
+[88] shinyWidgets_0.8.7 httr_1.4.7 GlobalOptions_0.1.2
+[91] statmod_1.5.0 mime_0.12
@@ -2760,7 +2759,7 @@ Key Points
Content from Differential expression analysis
- Last updated on 2024-12-03 |
+
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@@ -3453,7 +3452,7 @@ Key Points
Content from Extra exploration of design matrices
- Last updated on 2024-12-03 |
+
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@@ -3816,7 +3815,7 @@ Challenge
-
+
R
@@ -3903,7 +3902,7 @@ Challenge
-
+
R
@@ -5115,7 +5114,7 @@ Key Points
Content from Gene set enrichment analysis
- Last updated on 2024-12-03 |
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Last updated on 2025-01-07 |
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@@ -5711,9 +5710,9 @@ ROUTPUT
Unit: microseconds
- expr min lq mean median uq max neval
- fisher 242.563 244.937 262.70772 247.967 251.9505 1406.496 100
- hyper 1.492 1.693 2.33685 2.555 2.8555 6.101 100
+ expr min lq mean median uq max neval
+ fisher 242.642 249.1445 271.24591 252.195 262.1435 1561.651 100
+ hyper 1.473 1.7080 2.53325 2.720 2.9710 8.786 100
It is very astonishing that phyper() is hundreds of
times faster than fisher.test(). Main reason is in
@@ -5871,7 +5870,7 @@
Challenge
-
+
R
@@ -6528,7 +6527,7 @@ OUTPUT<
OUTPUT
---> Expected input gene ID: 73884,382007,13214,226356,208188,66197
+--> Expected input gene ID: 60597,11517,17864,100039030,54486,69496
OUTPUT
@@ -6812,19 +6811,19 @@ OUTPUT<
mmu04913 Ovarian steroidogenesis - Mus musculus (house mouse)
mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse)
GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
-mmu00590 16/460 89/9818 0.1797753 3.837030 5.960759 3.104291e-06
-mmu00591 12/460 55/9818 0.2181818 4.656759 6.029243 6.756868e-06
-mmu00565 11/460 48/9818 0.2291667 4.891214 5.991495 9.914058e-06
-mmu00592 8/460 25/9818 0.3200000 6.829913 6.470696 1.166851e-05
-mmu04913 12/460 64/9818 0.1875000 4.001902 5.341607 3.445424e-05
-mmu04061 14/460 95/9818 0.1473684 3.145355 4.658408 1.259362e-04
+mmu00590 16/451 89/9569 0.1797753 3.814345 5.932220 3.338144e-06
+mmu00591 12/451 55/9569 0.2181818 4.629228 6.002927 7.161290e-06
+mmu00565 11/451 48/9569 0.2291667 4.862297 5.965873 1.046503e-05
+mmu00592 8/451 25/9569 0.3200000 6.789534 6.446107 1.217181e-05
+mmu04913 12/451 64/9569 0.1875000 3.978243 5.316467 3.643828e-05
+mmu04061 14/451 95/9569 0.1473684 3.126759 4.633002 1.337191e-04
p.adjust qvalue
-mmu00590 0.0009101439 0.0007860892
-mmu00591 0.0009101439 0.0007860892
-mmu00565 0.0009101439 0.0007860892
-mmu00592 0.0009101439 0.0007860892
-mmu04913 0.0021499443 0.0018569019
-mmu04061 0.0065486813 0.0056560810
+mmu00590 0.0009494012 0.0008231987
+mmu00591 0.0009494012 0.0008231987
+mmu00565 0.0009494012 0.0008231987
+mmu00592 0.0009494012 0.0008231987
+mmu04913 0.0022737489 0.0019715029
+mmu04061 0.0069533935 0.0060290895
geneID
mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687
mmu00591 18783/211429/329502/78390/242546/18781/18784/13113/622127/232889/237625/11687
@@ -7547,7 +7546,7 @@ Key Points
Content from Next steps
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
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diff --git a/discuss.html b/discuss.html
index 0db76e87..0e41f595 100644
--- a/discuss.html
+++ b/discuss.html
@@ -265,7 +265,7 @@
Discussion
- Last updated on 2024-12-03 |
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@@ -333,7 +333,7 @@ Discussion
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/discuss.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/discuss.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/fig/04-exploratory-qc-rendered-pca-exercise-1.png b/fig/04-exploratory-qc-rendered-pca-exercise-1.png
index abd0ec56..b324fb87 100644
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diff --git a/fig/05-differential-expression-rendered-heatmap-time-1.png b/fig/05-differential-expression-rendered-heatmap-time-1.png
index f4a7b9fd..a1ca69dc 100644
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diff --git a/fig/07-gene-set-analysis-rendered-hypergeom-1.png b/fig/07-gene-set-analysis-rendered-hypergeom-1.png
index d7e4c9ef..2cdf231c 100644
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diff --git a/instructor/01-intro-to-rnaseq.html b/instructor/01-intro-to-rnaseq.html
index 9285fdf2..9c08dc2a 100644
--- a/instructor/01-intro-to-rnaseq.html
+++ b/instructor/01-intro-to-rnaseq.html
@@ -269,7 +269,7 @@
Introduction to RNA-seq
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
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@@ -648,7 +648,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/01-intro-to-rnaseq.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/01-intro-to-rnaseq.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/instructor/02-setup.html b/instructor/02-setup.html
index f315e831..0e5c30c6 100644
--- a/instructor/02-setup.html
+++ b/instructor/02-setup.html
@@ -279,7 +279,7 @@
RStudio Project and Experimental Data
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
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@@ -639,7 +639,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/02-setup.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/02-setup.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/instructor/03-import-annotate.html b/instructor/03-import-annotate.html
index 88c7f989..f53b411a 100644
--- a/instructor/03-import-annotate.html
+++ b/instructor/03-import-annotate.html
@@ -282,7 +282,7 @@
Importing and annotating quantified data into R
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
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@@ -516,7 +516,7 @@ Challenge: Discuss the following points with your neig
-
+
- In
counts, the rows are genes just like the rows in
rowranges. The columns in counts are the
@@ -634,7 +634,7 @@ Challenge
-
+
R
@@ -1010,7 +1010,7 @@ Challenge
-
+
R
@@ -1134,7 +1134,7 @@ Challenge: How to subset to mRNA genes
-
+
R
@@ -1322,7 +1322,7 @@ OUTPUT<
[13] BiocGenerics_0.50.0 knitr_1.49
loaded via a namespace (and not attached):
- [1] Matrix_1.7-1 bit_4.5.0 jsonlite_1.8.9
+ [1] Matrix_1.7-1 bit_4.5.0.1 jsonlite_1.8.9
[4] compiler_4.4.2 BiocManager_1.30.25 renv_1.0.11
[7] crayon_1.5.3 blob_1.2.4 Biostrings_2.72.1
[10] png_0.1-8 fastmap_1.2.0 yaml_2.3.10
@@ -1330,7 +1330,7 @@ OUTPUT<
[16] S4Arrays_1.4.1 DelayedArray_0.30.1 GenomeInfoDbData_1.2.12
[19] DBI_1.2.3 rlang_1.1.4 KEGGREST_1.44.1
[22] cachem_1.1.0 xfun_0.49 bit64_4.5.2
-[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.8
+[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.9
[28] cli_3.6.3 zlibbioc_1.50.0 grid_4.4.2
[31] vctrs_0.6.5 evaluate_1.0.1 abind_1.4-8
[34] httr_1.4.7 pkgconfig_2.0.3 tools_4.4.2
@@ -1407,7 +1407,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/03-import-annotate.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/03-import-annotate.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/instructor/04-exploratory-qc.html b/instructor/04-exploratory-qc.html
index f5002213..75040baf 100644
--- a/instructor/04-exploratory-qc.html
+++ b/instructor/04-exploratory-qc.html
@@ -283,7 +283,7 @@
Exploratory analysis and quality control
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -860,33 +860,32 @@ OUTPUT<
[7] mgcv_1.9-1 png_0.1-8 vctrs_0.6.5
[10] pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3
[13] fastmap_1.2.0 XVector_0.44.0 labeling_0.4.3
-[16] utf8_1.2.4 promises_1.3.2 shinyAce_0.4.3
-[19] UCSC.utils_1.0.0 preprocessCore_1.66.0 xfun_0.49
-[22] cachem_1.1.0 zlibbioc_1.50.0 jsonlite_1.8.9
-[25] listviewer_4.0.0 later_1.4.1 DelayedArray_0.30.1
-[28] BiocParallel_1.38.0 parallel_4.4.2 cluster_2.1.6
-[31] R6_2.5.1 bslib_0.8.0 limma_3.60.6
-[34] jquerylib_0.1.4 Rcpp_1.0.13-1 iterators_1.0.14
-[37] knitr_1.49 httpuv_1.6.15 Matrix_1.7-1
-[40] splines_4.4.2 igraph_2.1.1 tidyselect_1.2.1
-[43] abind_1.4-8 yaml_2.3.10 doParallel_1.0.17
-[46] codetools_0.2-20 affy_1.82.0 miniUI_0.1.1.1
-[49] lattice_0.22-6 tibble_3.2.1 shiny_1.9.1
-[52] withr_3.0.2 evaluate_1.0.1 circlize_0.4.16
-[55] pillar_1.9.0 affyio_1.74.0 BiocManager_1.30.25
-[58] renv_1.0.11 DT_0.33 foreach_1.5.2
-[61] shinyjs_2.1.0 generics_0.1.3 munsell_0.5.1
-[64] scales_1.3.0 xtable_1.8-4 glue_1.8.0
-[67] tools_4.4.2 colourpicker_1.3.0 locfit_1.5-9.10
-[70] colorspace_2.1-1 nlme_3.1-166 GenomeInfoDbData_1.2.12
-[73] vipor_0.4.7 cli_3.6.3 fansi_1.0.6
-[76] viridisLite_0.4.2 S4Arrays_1.4.1 dplyr_1.1.4
-[79] gtable_0.3.6 rintrojs_0.3.4 sass_0.4.9
-[82] digest_0.6.37 SparseArray_1.4.8 ggrepel_0.9.6
-[85] farver_2.1.2 rjson_0.2.23 htmlwidgets_1.6.4
-[88] htmltools_0.5.8.1 lifecycle_1.0.4 shinyWidgets_0.8.7
-[91] httr_1.4.7 GlobalOptions_0.1.2 statmod_1.5.0
-[94] mime_0.12
+[16] promises_1.3.2 shinyAce_0.4.3 UCSC.utils_1.0.0
+[19] preprocessCore_1.66.0 xfun_0.49 cachem_1.1.0
+[22] zlibbioc_1.50.0 jsonlite_1.8.9 listviewer_4.0.0
+[25] later_1.4.1 DelayedArray_0.30.1 BiocParallel_1.38.0
+[28] parallel_4.4.2 cluster_2.1.8 R6_2.5.1
+[31] bslib_0.8.0 limma_3.60.6 jquerylib_0.1.4
+[34] Rcpp_1.0.13-1 iterators_1.0.14 knitr_1.49
+[37] httpuv_1.6.15 Matrix_1.7-1 splines_4.4.2
+[40] igraph_2.1.2 tidyselect_1.2.1 abind_1.4-8
+[43] yaml_2.3.10 doParallel_1.0.17 codetools_0.2-20
+[46] affy_1.82.0 miniUI_0.1.1.1 lattice_0.22-6
+[49] tibble_3.2.1 shiny_1.10.0 withr_3.0.2
+[52] evaluate_1.0.1 circlize_0.4.16 pillar_1.10.0
+[55] affyio_1.74.0 BiocManager_1.30.25 renv_1.0.11
+[58] DT_0.33 foreach_1.5.2 shinyjs_2.1.0
+[61] generics_0.1.3 munsell_0.5.1 scales_1.3.0
+[64] xtable_1.8-4 glue_1.8.0 tools_4.4.2
+[67] colourpicker_1.3.0 locfit_1.5-9.10 colorspace_2.1-1
+[70] nlme_3.1-166 GenomeInfoDbData_1.2.12 vipor_0.4.7
+[73] cli_3.6.3 viridisLite_0.4.2 S4Arrays_1.4.1
+[76] dplyr_1.1.4 gtable_0.3.6 rintrojs_0.3.4
+[79] sass_0.4.9 digest_0.6.37 SparseArray_1.4.8
+[82] ggrepel_0.9.6 farver_2.1.2 rjson_0.2.23
+[85] htmlwidgets_1.6.4 htmltools_0.5.8.1 lifecycle_1.0.4
+[88] shinyWidgets_0.8.7 httr_1.4.7 GlobalOptions_0.1.2
+[91] statmod_1.5.0 mime_0.12
@@ -959,7 +958,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/04-exploratory-qc.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/04-exploratory-qc.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/instructor/05-differential-expression.html b/instructor/05-differential-expression.html
index 3e016ff5..a66e3f1b 100644
--- a/instructor/05-differential-expression.html
+++ b/instructor/05-differential-expression.html
@@ -283,7 +283,7 @@
Differential expression analysis
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -1068,7 +1068,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/05-differential-expression.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/05-differential-expression.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/instructor/06-extra-design.html b/instructor/06-extra-design.html
index ea874605..a58c835d 100644
--- a/instructor/06-extra-design.html
+++ b/instructor/06-extra-design.html
@@ -285,7 +285,7 @@
Extra exploration of design matrices
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -648,7 +648,7 @@ Challenge
-
+
R
@@ -734,7 +734,7 @@ Challenge
-
+
R
@@ -1981,7 +1981,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/06-extra-design.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/06-extra-design.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/instructor/07-gene-set-analysis.html b/instructor/07-gene-set-analysis.html
index c459f298..8aacc2f6 100644
--- a/instructor/07-gene-set-analysis.html
+++ b/instructor/07-gene-set-analysis.html
@@ -279,7 +279,7 @@
Gene set enrichment analysis
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -836,9 +836,9 @@ ROUTPUT
Unit: microseconds
- expr min lq mean median uq max neval
- fisher 242.563 244.937 262.70772 247.967 251.9505 1406.496 100
- hyper 1.492 1.693 2.33685 2.555 2.8555 6.101 100
+ expr min lq mean median uq max neval
+ fisher 242.642 249.1445 271.24591 252.195 262.1435 1561.651 100
+ hyper 1.473 1.7080 2.53325 2.720 2.9710 8.786 100
It is very astonishing that phyper() is hundreds of
times faster than fisher.test(). Main reason is in
@@ -992,7 +992,7 @@
Challenge
-
+
R
@@ -1613,7 +1613,7 @@ OUTPUT<
OUTPUT
---> Expected input gene ID: 73884,382007,13214,226356,208188,66197
+--> Expected input gene ID: 60597,11517,17864,100039030,54486,69496
OUTPUT
@@ -1890,19 +1890,19 @@ OUTPUT<
mmu04913 Ovarian steroidogenesis - Mus musculus (house mouse)
mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse)
GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
-mmu00590 16/460 89/9818 0.1797753 3.837030 5.960759 3.104291e-06
-mmu00591 12/460 55/9818 0.2181818 4.656759 6.029243 6.756868e-06
-mmu00565 11/460 48/9818 0.2291667 4.891214 5.991495 9.914058e-06
-mmu00592 8/460 25/9818 0.3200000 6.829913 6.470696 1.166851e-05
-mmu04913 12/460 64/9818 0.1875000 4.001902 5.341607 3.445424e-05
-mmu04061 14/460 95/9818 0.1473684 3.145355 4.658408 1.259362e-04
+mmu00590 16/451 89/9569 0.1797753 3.814345 5.932220 3.338144e-06
+mmu00591 12/451 55/9569 0.2181818 4.629228 6.002927 7.161290e-06
+mmu00565 11/451 48/9569 0.2291667 4.862297 5.965873 1.046503e-05
+mmu00592 8/451 25/9569 0.3200000 6.789534 6.446107 1.217181e-05
+mmu04913 12/451 64/9569 0.1875000 3.978243 5.316467 3.643828e-05
+mmu04061 14/451 95/9569 0.1473684 3.126759 4.633002 1.337191e-04
p.adjust qvalue
-mmu00590 0.0009101439 0.0007860892
-mmu00591 0.0009101439 0.0007860892
-mmu00565 0.0009101439 0.0007860892
-mmu00592 0.0009101439 0.0007860892
-mmu04913 0.0021499443 0.0018569019
-mmu04061 0.0065486813 0.0056560810
+mmu00590 0.0009494012 0.0008231987
+mmu00591 0.0009494012 0.0008231987
+mmu00565 0.0009494012 0.0008231987
+mmu00592 0.0009494012 0.0008231987
+mmu04913 0.0022737489 0.0019715029
+mmu04061 0.0069533935 0.0060290895
geneID
mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687
mmu00591 18783/211429/329502/78390/242546/18781/18784/13113/622127/232889/237625/11687
@@ -2649,7 +2649,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/07-gene-set-analysis.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/07-gene-set-analysis.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/instructor/08-next-steps.html b/instructor/08-next-steps.html
index 4add8482..64af17fa 100644
--- a/instructor/08-next-steps.html
+++ b/instructor/08-next-steps.html
@@ -277,7 +277,7 @@
Next steps
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -426,7 +426,7 @@ Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/08-next-steps.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/08-next-steps.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 260962dc..c9f71bae 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -265,7 +265,7 @@
Contributor Code of Conduct
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -342,7 +342,7 @@ Contributor Code of Conduct
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/CODE_OF_CONDUCT.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/CODE_OF_CONDUCT.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 727f172c..4e44032e 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -265,7 +265,7 @@
Licenses
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -390,7 +390,7 @@ Licenses
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/LICENSE.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/LICENSE.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/instructor/aio.html b/instructor/aio.html
index 03adc646..907a1420 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -331,7 +331,7 @@
Content from Introduction to RNA-seq
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
Estimated time 100 minutes
@@ -670,7 +670,7 @@ Key Points
Content from RStudio Project and Experimental Data
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
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Estimated time 30 minutes
@@ -1006,7 +1006,7 @@ Key Points
Content from Importing and annotating quantified data into R
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
Estimated time 120 minutes
@@ -1246,7 +1246,7 @@ Challenge: Discuss the following points with your neig
-
+
- In
counts, the rows are genes just like the rows in
@@ -1372,7 +1372,7 @@ Challenge
-
+
R
@@ -1750,7 +1750,7 @@ Challenge
-
+
R
@@ -1878,7 +1878,7 @@ Challenge: How to subset to mRNA genes
-
+
R
@@ -2075,7 +2075,7 @@ OUTPUT<
[13] BiocGenerics_0.50.0 knitr_1.49
loaded via a namespace (and not attached):
- [1] Matrix_1.7-1 bit_4.5.0 jsonlite_1.8.9
+ [1] Matrix_1.7-1 bit_4.5.0.1 jsonlite_1.8.9
[4] compiler_4.4.2 BiocManager_1.30.25 renv_1.0.11
[7] crayon_1.5.3 blob_1.2.4 Biostrings_2.72.1
[10] png_0.1-8 fastmap_1.2.0 yaml_2.3.10
@@ -2083,7 +2083,7 @@ OUTPUT<
[16] S4Arrays_1.4.1 DelayedArray_0.30.1 GenomeInfoDbData_1.2.12
[19] DBI_1.2.3 rlang_1.1.4 KEGGREST_1.44.1
[22] cachem_1.1.0 xfun_0.49 bit64_4.5.2
-[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.8
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[28] cli_3.6.3 zlibbioc_1.50.0 grid_4.4.2
[31] vctrs_0.6.5 evaluate_1.0.1 abind_1.4-8
[34] httr_1.4.7 pkgconfig_2.0.3 tools_4.4.2
@@ -2110,7 +2110,7 @@ Key Points
Content from Exploratory analysis and quality control
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
Estimated time 180 minutes
@@ -2717,33 +2717,32 @@ OUTPUT<
[7] mgcv_1.9-1 png_0.1-8 vctrs_0.6.5
[10] pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3
[13] fastmap_1.2.0 XVector_0.44.0 labeling_0.4.3
-[16] utf8_1.2.4 promises_1.3.2 shinyAce_0.4.3
-[19] UCSC.utils_1.0.0 preprocessCore_1.66.0 xfun_0.49
-[22] cachem_1.1.0 zlibbioc_1.50.0 jsonlite_1.8.9
-[25] listviewer_4.0.0 later_1.4.1 DelayedArray_0.30.1
-[28] BiocParallel_1.38.0 parallel_4.4.2 cluster_2.1.6
-[31] R6_2.5.1 bslib_0.8.0 limma_3.60.6
-[34] jquerylib_0.1.4 Rcpp_1.0.13-1 iterators_1.0.14
-[37] knitr_1.49 httpuv_1.6.15 Matrix_1.7-1
-[40] splines_4.4.2 igraph_2.1.1 tidyselect_1.2.1
-[43] abind_1.4-8 yaml_2.3.10 doParallel_1.0.17
-[46] codetools_0.2-20 affy_1.82.0 miniUI_0.1.1.1
-[49] lattice_0.22-6 tibble_3.2.1 shiny_1.9.1
-[52] withr_3.0.2 evaluate_1.0.1 circlize_0.4.16
-[55] pillar_1.9.0 affyio_1.74.0 BiocManager_1.30.25
-[58] renv_1.0.11 DT_0.33 foreach_1.5.2
-[61] shinyjs_2.1.0 generics_0.1.3 munsell_0.5.1
-[64] scales_1.3.0 xtable_1.8-4 glue_1.8.0
-[67] tools_4.4.2 colourpicker_1.3.0 locfit_1.5-9.10
-[70] colorspace_2.1-1 nlme_3.1-166 GenomeInfoDbData_1.2.12
-[73] vipor_0.4.7 cli_3.6.3 fansi_1.0.6
-[76] viridisLite_0.4.2 S4Arrays_1.4.1 dplyr_1.1.4
-[79] gtable_0.3.6 rintrojs_0.3.4 sass_0.4.9
-[82] digest_0.6.37 SparseArray_1.4.8 ggrepel_0.9.6
-[85] farver_2.1.2 rjson_0.2.23 htmlwidgets_1.6.4
-[88] htmltools_0.5.8.1 lifecycle_1.0.4 shinyWidgets_0.8.7
-[91] httr_1.4.7 GlobalOptions_0.1.2 statmod_1.5.0
-[94] mime_0.12
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+[34] Rcpp_1.0.13-1 iterators_1.0.14 knitr_1.49
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+[49] tibble_3.2.1 shiny_1.10.0 withr_3.0.2
+[52] evaluate_1.0.1 circlize_0.4.16 pillar_1.10.0
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+[58] DT_0.33 foreach_1.5.2 shinyjs_2.1.0
+[61] generics_0.1.3 munsell_0.5.1 scales_1.3.0
+[64] xtable_1.8-4 glue_1.8.0 tools_4.4.2
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+[70] nlme_3.1-166 GenomeInfoDbData_1.2.12 vipor_0.4.7
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+[76] dplyr_1.1.4 gtable_0.3.6 rintrojs_0.3.4
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+[82] ggrepel_0.9.6 farver_2.1.2 rjson_0.2.23
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+[88] shinyWidgets_0.8.7 httr_1.4.7 GlobalOptions_0.1.2
+[91] statmod_1.5.0 mime_0.12
Key Points
Content from Differential expression analysis
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
Estimated time 105 minutes
@@ -3522,7 +3521,7 @@ Key Points
Content from Extra exploration of design matrices
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
Estimated time 60 minutes
@@ -3886,7 +3885,7 @@ Challenge
-
+
R
@@ -3973,7 +3972,7 @@ Challenge
-
+
R
@@ -5185,7 +5184,7 @@ Key Points
Content from Gene set enrichment analysis
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
Estimated time 105 minutes
@@ -5782,9 +5781,9 @@ ROUTPUT
Unit: microseconds
- expr min lq mean median uq max neval
- fisher 242.563 244.937 262.70772 247.967 251.9505 1406.496 100
- hyper 1.492 1.693 2.33685 2.555 2.8555 6.101 100
+ expr min lq mean median uq max neval
+ fisher 242.642 249.1445 271.24591 252.195 262.1435 1561.651 100
+ hyper 1.473 1.7080 2.53325 2.720 2.9710 8.786 100
It is very astonishing that phyper() is hundreds of
times faster than fisher.test(). Main reason is in
@@ -5942,7 +5941,7 @@
Challenge
-
+
R
@@ -6599,7 +6598,7 @@ OUTPUT<
OUTPUT
---> Expected input gene ID: 73884,382007,13214,226356,208188,66197
+--> Expected input gene ID: 60597,11517,17864,100039030,54486,69496
OUTPUT
@@ -6883,19 +6882,19 @@ OUTPUT<
mmu04913 Ovarian steroidogenesis - Mus musculus (house mouse)
mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse)
GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
-mmu00590 16/460 89/9818 0.1797753 3.837030 5.960759 3.104291e-06
-mmu00591 12/460 55/9818 0.2181818 4.656759 6.029243 6.756868e-06
-mmu00565 11/460 48/9818 0.2291667 4.891214 5.991495 9.914058e-06
-mmu00592 8/460 25/9818 0.3200000 6.829913 6.470696 1.166851e-05
-mmu04913 12/460 64/9818 0.1875000 4.001902 5.341607 3.445424e-05
-mmu04061 14/460 95/9818 0.1473684 3.145355 4.658408 1.259362e-04
+mmu00590 16/451 89/9569 0.1797753 3.814345 5.932220 3.338144e-06
+mmu00591 12/451 55/9569 0.2181818 4.629228 6.002927 7.161290e-06
+mmu00565 11/451 48/9569 0.2291667 4.862297 5.965873 1.046503e-05
+mmu00592 8/451 25/9569 0.3200000 6.789534 6.446107 1.217181e-05
+mmu04913 12/451 64/9569 0.1875000 3.978243 5.316467 3.643828e-05
+mmu04061 14/451 95/9569 0.1473684 3.126759 4.633002 1.337191e-04
p.adjust qvalue
-mmu00590 0.0009101439 0.0007860892
-mmu00591 0.0009101439 0.0007860892
-mmu00565 0.0009101439 0.0007860892
-mmu00592 0.0009101439 0.0007860892
-mmu04913 0.0021499443 0.0018569019
-mmu04061 0.0065486813 0.0056560810
+mmu00590 0.0009494012 0.0008231987
+mmu00591 0.0009494012 0.0008231987
+mmu00565 0.0009494012 0.0008231987
+mmu00592 0.0009494012 0.0008231987
+mmu04913 0.0022737489 0.0019715029
+mmu04061 0.0069533935 0.0060290895
geneID
mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687
mmu00591 18783/211429/329502/78390/242546/18781/18784/13113/622127/232889/237625/11687
@@ -7618,7 +7617,7 @@ Key Points
Content from Next steps
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
Estimated time 20 minutes
diff --git a/instructor/discuss.html b/instructor/discuss.html
index 6d621c24..e6a61a9b 100644
--- a/instructor/discuss.html
+++ b/instructor/discuss.html
@@ -265,7 +265,7 @@
Discussion
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -335,7 +335,7 @@ Discussion
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/discuss.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/discuss.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
diff --git a/instructor/reference.html b/instructor/reference.html
index 9a3f6e97..6b69585e 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -265,7 +265,7 @@
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -334,7 +334,7 @@
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/reference.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/reference.html",
"dateCreated": "2020-09-15",
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"datePublished": "2025-01-07"
}
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index df098712..40573f87 100644
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diff --git a/pkgdown.yml b/pkgdown.yml
index 43c8bf73..668380b3 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
pkgdown: 2.1.1
pkgdown_sha: ~
articles: {}
-last_built: 2025-01-07T00:54Z
+last_built: 2025-01-07T07:51Z
diff --git a/reference.html b/reference.html
index ef2c1262..642d3855 100644
--- a/reference.html
+++ b/reference.html
@@ -265,7 +265,7 @@
- Last updated on 2024-12-03 |
+
Last updated on 2025-01-07 |
Edit this page
@@ -332,7 +332,7 @@
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/reference.html",
"identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/reference.html",
"dateCreated": "2020-09-15",
- "dateModified": "2024-12-03",
+ "dateModified": "2025-01-07",
"datePublished": "2025-01-07"
}
- In
counts, the rows are genes just like the rows inrowranges. The columns incountsare the @@ -632,7 +632,7 @@Challenge
-+R @@ -1008,7 +1008,7 @@
Challenge
-+R @@ -1132,7 +1132,7 @@
Challenge: How to subset to mRNA genes
-+R @@ -1320,7 +1320,7 @@
OUTPUT< [13] BiocGenerics_0.50.0 knitr_1.49 loaded via a namespace (and not attached): - [1] Matrix_1.7-1 bit_4.5.0 jsonlite_1.8.9 + [1] Matrix_1.7-1 bit_4.5.0.1 jsonlite_1.8.9 [4] compiler_4.4.2 BiocManager_1.30.25 renv_1.0.11 [7] crayon_1.5.3 blob_1.2.4 Biostrings_2.72.1 [10] png_0.1-8 fastmap_1.2.0 yaml_2.3.10 @@ -1328,7 +1328,7 @@
OUTPUT< [16] S4Arrays_1.4.1 DelayedArray_0.30.1 GenomeInfoDbData_1.2.12 [19] DBI_1.2.3 rlang_1.1.4 KEGGREST_1.44.1 [22] cachem_1.1.0 xfun_0.49 bit64_4.5.2 -[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.8 +[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.9 [28] cli_3.6.3 zlibbioc_1.50.0 grid_4.4.2 [31] vctrs_0.6.5 evaluate_1.0.1 abind_1.4-8 [34] httr_1.4.7 pkgconfig_2.0.3 tools_4.4.2 @@ -1405,7 +1405,7 @@
Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/03-import-annotate.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/03-import-annotate.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/04-exploratory-qc.html b/04-exploratory-qc.html index f7175e2a..499fcf65 100644 --- a/04-exploratory-qc.html +++ b/04-exploratory-qc.html @@ -283,7 +283,7 @@Exploratory analysis and quality control
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
@@ -858,33 +858,32 @@OUTPUT< [7] mgcv_1.9-1 png_0.1-8 vctrs_0.6.5 [10] pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3 [13] fastmap_1.2.0 XVector_0.44.0 labeling_0.4.3 -[16] utf8_1.2.4 promises_1.3.2 shinyAce_0.4.3 -[19] UCSC.utils_1.0.0 preprocessCore_1.66.0 xfun_0.49 -[22] cachem_1.1.0 zlibbioc_1.50.0 jsonlite_1.8.9 -[25] listviewer_4.0.0 later_1.4.1 DelayedArray_0.30.1 -[28] BiocParallel_1.38.0 parallel_4.4.2 cluster_2.1.6 -[31] R6_2.5.1 bslib_0.8.0 limma_3.60.6 -[34] jquerylib_0.1.4 Rcpp_1.0.13-1 iterators_1.0.14 -[37] knitr_1.49 httpuv_1.6.15 Matrix_1.7-1 -[40] splines_4.4.2 igraph_2.1.1 tidyselect_1.2.1 -[43] abind_1.4-8 yaml_2.3.10 doParallel_1.0.17 -[46] codetools_0.2-20 affy_1.82.0 miniUI_0.1.1.1 -[49] lattice_0.22-6 tibble_3.2.1 shiny_1.9.1 -[52] withr_3.0.2 evaluate_1.0.1 circlize_0.4.16 -[55] pillar_1.9.0 affyio_1.74.0 BiocManager_1.30.25 -[58] renv_1.0.11 DT_0.33 foreach_1.5.2 -[61] shinyjs_2.1.0 generics_0.1.3 munsell_0.5.1 -[64] scales_1.3.0 xtable_1.8-4 glue_1.8.0 -[67] tools_4.4.2 colourpicker_1.3.0 locfit_1.5-9.10 -[70] colorspace_2.1-1 nlme_3.1-166 GenomeInfoDbData_1.2.12 -[73] vipor_0.4.7 cli_3.6.3 fansi_1.0.6 -[76] viridisLite_0.4.2 S4Arrays_1.4.1 dplyr_1.1.4 -[79] gtable_0.3.6 rintrojs_0.3.4 sass_0.4.9 -[82] digest_0.6.37 SparseArray_1.4.8 ggrepel_0.9.6 -[85] farver_2.1.2 rjson_0.2.23 htmlwidgets_1.6.4 -[88] htmltools_0.5.8.1 lifecycle_1.0.4 shinyWidgets_0.8.7 -[91] httr_1.4.7 GlobalOptions_0.1.2 statmod_1.5.0 -[94] mime_0.12 +[16] promises_1.3.2 shinyAce_0.4.3 UCSC.utils_1.0.0 +[19] preprocessCore_1.66.0 xfun_0.49 cachem_1.1.0 +[22] zlibbioc_1.50.0 jsonlite_1.8.9 listviewer_4.0.0 +[25] later_1.4.1 DelayedArray_0.30.1 BiocParallel_1.38.0 +[28] parallel_4.4.2 cluster_2.1.8 R6_2.5.1 +[31] bslib_0.8.0 limma_3.60.6 jquerylib_0.1.4 +[34] Rcpp_1.0.13-1 iterators_1.0.14 knitr_1.49 +[37] httpuv_1.6.15 Matrix_1.7-1 splines_4.4.2 +[40] igraph_2.1.2 tidyselect_1.2.1 abind_1.4-8 +[43] yaml_2.3.10 doParallel_1.0.17 codetools_0.2-20 +[46] affy_1.82.0 miniUI_0.1.1.1 lattice_0.22-6 +[49] tibble_3.2.1 shiny_1.10.0 withr_3.0.2 +[52] evaluate_1.0.1 circlize_0.4.16 pillar_1.10.0 +[55] affyio_1.74.0 BiocManager_1.30.25 renv_1.0.11 +[58] DT_0.33 foreach_1.5.2 shinyjs_2.1.0 +[61] generics_0.1.3 munsell_0.5.1 scales_1.3.0 +[64] xtable_1.8-4 glue_1.8.0 tools_4.4.2 +[67] colourpicker_1.3.0 locfit_1.5-9.10 colorspace_2.1-1 +[70] nlme_3.1-166 GenomeInfoDbData_1.2.12 vipor_0.4.7 +[73] cli_3.6.3 viridisLite_0.4.2 S4Arrays_1.4.1 +[76] dplyr_1.1.4 gtable_0.3.6 rintrojs_0.3.4 +[79] sass_0.4.9 digest_0.6.37 SparseArray_1.4.8 +[82] ggrepel_0.9.6 farver_2.1.2 rjson_0.2.23 +[85] htmlwidgets_1.6.4 htmltools_0.5.8.1 lifecycle_1.0.4 +[88] shinyWidgets_0.8.7 httr_1.4.7 GlobalOptions_0.1.2 +[91] statmod_1.5.0 mime_0.12
@@ -957,7 +956,7 @@Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/04-exploratory-qc.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/04-exploratory-qc.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/05-differential-expression.html b/05-differential-expression.html index 7f152fb0..c95f9d53 100644 --- a/05-differential-expression.html +++ b/05-differential-expression.html @@ -283,7 +283,7 @@Differential expression analysis
-Last updated on 2024-12-03 | +
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@@ -1004,7 +1004,7 @@Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/05-differential-expression.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/05-differential-expression.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/06-extra-design.html b/06-extra-design.html index 9b93676c..31e5037c 100644 --- a/06-extra-design.html +++ b/06-extra-design.html @@ -285,7 +285,7 @@Extra exploration of design matrices
-Last updated on 2024-12-03 | +
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@@ -646,7 +646,7 @@Challenge
-+R @@ -732,7 +732,7 @@
Challenge
-+R @@ -1979,7 +1979,7 @@
Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/06-extra-design.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/06-extra-design.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/07-gene-set-analysis.html b/07-gene-set-analysis.html index 04844a20..c7e48425 100644 --- a/07-gene-set-analysis.html +++ b/07-gene-set-analysis.html @@ -279,7 +279,7 @@Gene set enrichment analysis
-Last updated on 2024-12-03 | +
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@@ -834,9 +834,9 @@ROUTPUT
+ expr min lq mean median uq max neval + fisher 242.642 249.1445 271.24591 252.195 262.1435 1561.651 100 + hyper 1.473 1.7080 2.53325 2.720 2.9710 8.786 100Unit: microseconds - expr min lq mean median uq max neval - fisher 242.563 244.937 262.70772 247.967 251.9505 1406.496 100 - hyper 1.492 1.693 2.33685 2.555 2.8555 6.101 100It is very astonishing that
phyper()is hundreds of times faster thanfisher.test(). Main reason is in @@ -990,7 +990,7 @@Challenge
-+R @@ -1611,7 +1611,7 @@
OUTPUT<
OUTPUT
-
+--> Expected input gene ID: 73884,382007,13214,226356,208188,66197--> Expected input gene ID: 60597,11517,17864,100039030,54486,69496OUTPUT @@ -1888,19 +1888,19 @@
OUTPUT< mmu04913 Ovarian steroidogenesis - Mus musculus (house mouse) mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse) GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue -mmu00590 16/460 89/9818 0.1797753 3.837030 5.960759 3.104291e-06 -mmu00591 12/460 55/9818 0.2181818 4.656759 6.029243 6.756868e-06 -mmu00565 11/460 48/9818 0.2291667 4.891214 5.991495 9.914058e-06 -mmu00592 8/460 25/9818 0.3200000 6.829913 6.470696 1.166851e-05 -mmu04913 12/460 64/9818 0.1875000 4.001902 5.341607 3.445424e-05 -mmu04061 14/460 95/9818 0.1473684 3.145355 4.658408 1.259362e-04 +mmu00590 16/451 89/9569 0.1797753 3.814345 5.932220 3.338144e-06 +mmu00591 12/451 55/9569 0.2181818 4.629228 6.002927 7.161290e-06 +mmu00565 11/451 48/9569 0.2291667 4.862297 5.965873 1.046503e-05 +mmu00592 8/451 25/9569 0.3200000 6.789534 6.446107 1.217181e-05 +mmu04913 12/451 64/9569 0.1875000 3.978243 5.316467 3.643828e-05 +mmu04061 14/451 95/9569 0.1473684 3.126759 4.633002 1.337191e-04 p.adjust qvalue -mmu00590 0.0009101439 0.0007860892 -mmu00591 0.0009101439 0.0007860892 -mmu00565 0.0009101439 0.0007860892 -mmu00592 0.0009101439 0.0007860892 -mmu04913 0.0021499443 0.0018569019 -mmu04061 0.0065486813 0.0056560810 +mmu00590 0.0009494012 0.0008231987 +mmu00591 0.0009494012 0.0008231987 +mmu00565 0.0009494012 0.0008231987 +mmu00592 0.0009494012 0.0008231987 +mmu04913 0.0022737489 0.0019715029 +mmu04061 0.0069533935 0.0060290895 geneID mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687 mmu00591 18783/211429/329502/78390/242546/18781/18784/13113/622127/232889/237625/11687 @@ -2647,7 +2647,7 @@
Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/07-gene-set-analysis.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/07-gene-set-analysis.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/08-next-steps.html b/08-next-steps.html index 3db185ab..8de922a1 100644 --- a/08-next-steps.html +++ b/08-next-steps.html @@ -277,7 +277,7 @@Next steps
-Last updated on 2024-12-03 | +
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@@ -424,7 +424,7 @@Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/08-next-steps.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/08-next-steps.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index acd53dca..8bc758e6 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -265,7 +265,7 @@Contributor Code of Conduct
-Last updated on 2024-12-03 | +
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@@ -340,7 +340,7 @@Contributor Code of Conduct
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/CODE_OF_CONDUCT.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/CODE_OF_CONDUCT.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/LICENSE.html b/LICENSE.html index 5ed6a5e1..97896f52 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -265,7 +265,7 @@Licenses
-Last updated on 2024-12-03 | +
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@@ -388,7 +388,7 @@Licenses
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/LICENSE.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/LICENSE.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/aio.html b/aio.html index b4085f05..46eb54f0 100644 --- a/aio.html +++ b/aio.html @@ -329,7 +329,7 @@Content from Introduction to RNA-seq
-Last updated on 2024-12-03 | +
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@@ -667,7 +667,7 @@Key Points
Content from RStudio Project and Experimental Data
-Last updated on 2024-12-03 | +
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@@ -1002,7 +1002,7 @@Key Points
Content from Importing and annotating quantified data into R
-Last updated on 2024-12-03 | +
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@@ -1241,7 +1241,7 @@Challenge: Discuss the following points with your neig -
+- In
counts, the rows are genes just like the rows in @@ -1367,7 +1367,7 @@Challenge
-+R @@ -1745,7 +1745,7 @@
Challenge
-+R @@ -1873,7 +1873,7 @@
Challenge: How to subset to mRNA genes
-+R @@ -2070,7 +2070,7 @@
OUTPUT< [13] BiocGenerics_0.50.0 knitr_1.49 loaded via a namespace (and not attached): - [1] Matrix_1.7-1 bit_4.5.0 jsonlite_1.8.9 + [1] Matrix_1.7-1 bit_4.5.0.1 jsonlite_1.8.9 [4] compiler_4.4.2 BiocManager_1.30.25 renv_1.0.11 [7] crayon_1.5.3 blob_1.2.4 Biostrings_2.72.1 [10] png_0.1-8 fastmap_1.2.0 yaml_2.3.10 @@ -2078,7 +2078,7 @@
OUTPUT< [16] S4Arrays_1.4.1 DelayedArray_0.30.1 GenomeInfoDbData_1.2.12 [19] DBI_1.2.3 rlang_1.1.4 KEGGREST_1.44.1 [22] cachem_1.1.0 xfun_0.49 bit64_4.5.2 -[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.8 +[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.9 [28] cli_3.6.3 zlibbioc_1.50.0 grid_4.4.2 [31] vctrs_0.6.5 evaluate_1.0.1 abind_1.4-8 [34] httr_1.4.7 pkgconfig_2.0.3 tools_4.4.2 @@ -2105,7 +2105,7 @@
Key Points
Content from Exploratory analysis and quality control
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
@@ -2711,33 +2711,32 @@OUTPUT< [7] mgcv_1.9-1 png_0.1-8 vctrs_0.6.5 [10] pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3 [13] fastmap_1.2.0 XVector_0.44.0 labeling_0.4.3 -[16] utf8_1.2.4 promises_1.3.2 shinyAce_0.4.3 -[19] UCSC.utils_1.0.0 preprocessCore_1.66.0 xfun_0.49 -[22] cachem_1.1.0 zlibbioc_1.50.0 jsonlite_1.8.9 -[25] listviewer_4.0.0 later_1.4.1 DelayedArray_0.30.1 -[28] BiocParallel_1.38.0 parallel_4.4.2 cluster_2.1.6 -[31] R6_2.5.1 bslib_0.8.0 limma_3.60.6 -[34] jquerylib_0.1.4 Rcpp_1.0.13-1 iterators_1.0.14 -[37] knitr_1.49 httpuv_1.6.15 Matrix_1.7-1 -[40] splines_4.4.2 igraph_2.1.1 tidyselect_1.2.1 -[43] abind_1.4-8 yaml_2.3.10 doParallel_1.0.17 -[46] codetools_0.2-20 affy_1.82.0 miniUI_0.1.1.1 -[49] lattice_0.22-6 tibble_3.2.1 shiny_1.9.1 -[52] withr_3.0.2 evaluate_1.0.1 circlize_0.4.16 -[55] pillar_1.9.0 affyio_1.74.0 BiocManager_1.30.25 -[58] renv_1.0.11 DT_0.33 foreach_1.5.2 -[61] shinyjs_2.1.0 generics_0.1.3 munsell_0.5.1 -[64] scales_1.3.0 xtable_1.8-4 glue_1.8.0 -[67] tools_4.4.2 colourpicker_1.3.0 locfit_1.5-9.10 -[70] colorspace_2.1-1 nlme_3.1-166 GenomeInfoDbData_1.2.12 -[73] vipor_0.4.7 cli_3.6.3 fansi_1.0.6 -[76] viridisLite_0.4.2 S4Arrays_1.4.1 dplyr_1.1.4 -[79] gtable_0.3.6 rintrojs_0.3.4 sass_0.4.9 -[82] digest_0.6.37 SparseArray_1.4.8 ggrepel_0.9.6 -[85] farver_2.1.2 rjson_0.2.23 htmlwidgets_1.6.4 -[88] htmltools_0.5.8.1 lifecycle_1.0.4 shinyWidgets_0.8.7 -[91] httr_1.4.7 GlobalOptions_0.1.2 statmod_1.5.0 -[94] mime_0.12 +[16] promises_1.3.2 shinyAce_0.4.3 UCSC.utils_1.0.0 +[19] preprocessCore_1.66.0 xfun_0.49 cachem_1.1.0 +[22] zlibbioc_1.50.0 jsonlite_1.8.9 listviewer_4.0.0 +[25] later_1.4.1 DelayedArray_0.30.1 BiocParallel_1.38.0 +[28] parallel_4.4.2 cluster_2.1.8 R6_2.5.1 +[31] bslib_0.8.0 limma_3.60.6 jquerylib_0.1.4 +[34] Rcpp_1.0.13-1 iterators_1.0.14 knitr_1.49 +[37] httpuv_1.6.15 Matrix_1.7-1 splines_4.4.2 +[40] igraph_2.1.2 tidyselect_1.2.1 abind_1.4-8 +[43] yaml_2.3.10 doParallel_1.0.17 codetools_0.2-20 +[46] affy_1.82.0 miniUI_0.1.1.1 lattice_0.22-6 +[49] tibble_3.2.1 shiny_1.10.0 withr_3.0.2 +[52] evaluate_1.0.1 circlize_0.4.16 pillar_1.10.0 +[55] affyio_1.74.0 BiocManager_1.30.25 renv_1.0.11 +[58] DT_0.33 foreach_1.5.2 shinyjs_2.1.0 +[61] generics_0.1.3 munsell_0.5.1 scales_1.3.0 +[64] xtable_1.8-4 glue_1.8.0 tools_4.4.2 +[67] colourpicker_1.3.0 locfit_1.5-9.10 colorspace_2.1-1 +[70] nlme_3.1-166 GenomeInfoDbData_1.2.12 vipor_0.4.7 +[73] cli_3.6.3 viridisLite_0.4.2 S4Arrays_1.4.1 +[76] dplyr_1.1.4 gtable_0.3.6 rintrojs_0.3.4 +[79] sass_0.4.9 digest_0.6.37 SparseArray_1.4.8 +[82] ggrepel_0.9.6 farver_2.1.2 rjson_0.2.23 +[85] htmlwidgets_1.6.4 htmltools_0.5.8.1 lifecycle_1.0.4 +[88] shinyWidgets_0.8.7 httr_1.4.7 GlobalOptions_0.1.2 +[91] statmod_1.5.0 mime_0.12
@@ -2760,7 +2759,7 @@Key Points
Content from Differential expression analysis
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
@@ -3453,7 +3452,7 @@Key Points
Content from Extra exploration of design matrices
-Last updated on 2024-12-03 | +
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@@ -3816,7 +3815,7 @@Challenge
-+R @@ -3903,7 +3902,7 @@
Challenge
-+R @@ -5115,7 +5114,7 @@
Key Points
Content from Gene set enrichment analysis
-Last updated on 2024-12-03 | +
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@@ -5711,9 +5710,9 @@ROUTPUT
+ expr min lq mean median uq max neval + fisher 242.642 249.1445 271.24591 252.195 262.1435 1561.651 100 + hyper 1.473 1.7080 2.53325 2.720 2.9710 8.786 100Unit: microseconds - expr min lq mean median uq max neval - fisher 242.563 244.937 262.70772 247.967 251.9505 1406.496 100 - hyper 1.492 1.693 2.33685 2.555 2.8555 6.101 100It is very astonishing that
phyper()is hundreds of times faster thanfisher.test(). Main reason is in @@ -5871,7 +5870,7 @@Challenge
-+R @@ -6528,7 +6527,7 @@
OUTPUT<
OUTPUT
-
+--> Expected input gene ID: 73884,382007,13214,226356,208188,66197--> Expected input gene ID: 60597,11517,17864,100039030,54486,69496OUTPUT @@ -6812,19 +6811,19 @@
OUTPUT< mmu04913 Ovarian steroidogenesis - Mus musculus (house mouse) mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse) GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue -mmu00590 16/460 89/9818 0.1797753 3.837030 5.960759 3.104291e-06 -mmu00591 12/460 55/9818 0.2181818 4.656759 6.029243 6.756868e-06 -mmu00565 11/460 48/9818 0.2291667 4.891214 5.991495 9.914058e-06 -mmu00592 8/460 25/9818 0.3200000 6.829913 6.470696 1.166851e-05 -mmu04913 12/460 64/9818 0.1875000 4.001902 5.341607 3.445424e-05 -mmu04061 14/460 95/9818 0.1473684 3.145355 4.658408 1.259362e-04 +mmu00590 16/451 89/9569 0.1797753 3.814345 5.932220 3.338144e-06 +mmu00591 12/451 55/9569 0.2181818 4.629228 6.002927 7.161290e-06 +mmu00565 11/451 48/9569 0.2291667 4.862297 5.965873 1.046503e-05 +mmu00592 8/451 25/9569 0.3200000 6.789534 6.446107 1.217181e-05 +mmu04913 12/451 64/9569 0.1875000 3.978243 5.316467 3.643828e-05 +mmu04061 14/451 95/9569 0.1473684 3.126759 4.633002 1.337191e-04 p.adjust qvalue -mmu00590 0.0009101439 0.0007860892 -mmu00591 0.0009101439 0.0007860892 -mmu00565 0.0009101439 0.0007860892 -mmu00592 0.0009101439 0.0007860892 -mmu04913 0.0021499443 0.0018569019 -mmu04061 0.0065486813 0.0056560810 +mmu00590 0.0009494012 0.0008231987 +mmu00591 0.0009494012 0.0008231987 +mmu00565 0.0009494012 0.0008231987 +mmu00592 0.0009494012 0.0008231987 +mmu04913 0.0022737489 0.0019715029 +mmu04061 0.0069533935 0.0060290895 geneID mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687 mmu00591 18783/211429/329502/78390/242546/18781/18784/13113/622127/232889/237625/11687 @@ -7547,7 +7546,7 @@
Key Points
Content from Next steps
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
diff --git a/discuss.html b/discuss.html index 0db76e87..0e41f595 100644 --- a/discuss.html +++ b/discuss.html @@ -265,7 +265,7 @@Discussion
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@@ -333,7 +333,7 @@Discussion
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/discuss.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/discuss.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/fig/04-exploratory-qc-rendered-pca-exercise-1.png b/fig/04-exploratory-qc-rendered-pca-exercise-1.png index abd0ec56..b324fb87 100644 Binary files a/fig/04-exploratory-qc-rendered-pca-exercise-1.png and b/fig/04-exploratory-qc-rendered-pca-exercise-1.png differ diff --git a/fig/05-differential-expression-rendered-heatmap-time-1.png b/fig/05-differential-expression-rendered-heatmap-time-1.png index f4a7b9fd..a1ca69dc 100644 Binary files a/fig/05-differential-expression-rendered-heatmap-time-1.png and b/fig/05-differential-expression-rendered-heatmap-time-1.png differ diff --git a/fig/07-gene-set-analysis-rendered-hypergeom-1.png b/fig/07-gene-set-analysis-rendered-hypergeom-1.png index d7e4c9ef..2cdf231c 100644 Binary files a/fig/07-gene-set-analysis-rendered-hypergeom-1.png and b/fig/07-gene-set-analysis-rendered-hypergeom-1.png differ diff --git a/instructor/01-intro-to-rnaseq.html b/instructor/01-intro-to-rnaseq.html index 9285fdf2..9c08dc2a 100644 --- a/instructor/01-intro-to-rnaseq.html +++ b/instructor/01-intro-to-rnaseq.html @@ -269,7 +269,7 @@Introduction to RNA-seq
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
@@ -648,7 +648,7 @@Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/01-intro-to-rnaseq.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/01-intro-to-rnaseq.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/instructor/02-setup.html b/instructor/02-setup.html index f315e831..0e5c30c6 100644 --- a/instructor/02-setup.html +++ b/instructor/02-setup.html @@ -279,7 +279,7 @@RStudio Project and Experimental Data
-Last updated on 2024-12-03 | +
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@@ -639,7 +639,7 @@Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/02-setup.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/02-setup.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/instructor/03-import-annotate.html b/instructor/03-import-annotate.html index 88c7f989..f53b411a 100644 --- a/instructor/03-import-annotate.html +++ b/instructor/03-import-annotate.html @@ -282,7 +282,7 @@Importing and annotating quantified data into R
-Last updated on 2024-12-03 | +
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@@ -516,7 +516,7 @@Challenge: Discuss the following points with your neig -
+- In
counts, the rows are genes just like the rows inrowranges. The columns incountsare the @@ -634,7 +634,7 @@Challenge
-+R @@ -1010,7 +1010,7 @@
Challenge
-+R @@ -1134,7 +1134,7 @@
Challenge: How to subset to mRNA genes
-+R @@ -1322,7 +1322,7 @@
OUTPUT< [13] BiocGenerics_0.50.0 knitr_1.49 loaded via a namespace (and not attached): - [1] Matrix_1.7-1 bit_4.5.0 jsonlite_1.8.9 + [1] Matrix_1.7-1 bit_4.5.0.1 jsonlite_1.8.9 [4] compiler_4.4.2 BiocManager_1.30.25 renv_1.0.11 [7] crayon_1.5.3 blob_1.2.4 Biostrings_2.72.1 [10] png_0.1-8 fastmap_1.2.0 yaml_2.3.10 @@ -1330,7 +1330,7 @@
OUTPUT< [16] S4Arrays_1.4.1 DelayedArray_0.30.1 GenomeInfoDbData_1.2.12 [19] DBI_1.2.3 rlang_1.1.4 KEGGREST_1.44.1 [22] cachem_1.1.0 xfun_0.49 bit64_4.5.2 -[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.8 +[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.9 [28] cli_3.6.3 zlibbioc_1.50.0 grid_4.4.2 [31] vctrs_0.6.5 evaluate_1.0.1 abind_1.4-8 [34] httr_1.4.7 pkgconfig_2.0.3 tools_4.4.2 @@ -1407,7 +1407,7 @@
Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/03-import-annotate.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/03-import-annotate.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/instructor/04-exploratory-qc.html b/instructor/04-exploratory-qc.html index f5002213..75040baf 100644 --- a/instructor/04-exploratory-qc.html +++ b/instructor/04-exploratory-qc.html @@ -283,7 +283,7 @@Exploratory analysis and quality control
-Last updated on 2024-12-03 | +
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@@ -860,33 +860,32 @@OUTPUT< [7] mgcv_1.9-1 png_0.1-8 vctrs_0.6.5 [10] pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3 [13] fastmap_1.2.0 XVector_0.44.0 labeling_0.4.3 -[16] utf8_1.2.4 promises_1.3.2 shinyAce_0.4.3 -[19] UCSC.utils_1.0.0 preprocessCore_1.66.0 xfun_0.49 -[22] cachem_1.1.0 zlibbioc_1.50.0 jsonlite_1.8.9 -[25] listviewer_4.0.0 later_1.4.1 DelayedArray_0.30.1 -[28] BiocParallel_1.38.0 parallel_4.4.2 cluster_2.1.6 -[31] R6_2.5.1 bslib_0.8.0 limma_3.60.6 -[34] jquerylib_0.1.4 Rcpp_1.0.13-1 iterators_1.0.14 -[37] knitr_1.49 httpuv_1.6.15 Matrix_1.7-1 -[40] splines_4.4.2 igraph_2.1.1 tidyselect_1.2.1 -[43] abind_1.4-8 yaml_2.3.10 doParallel_1.0.17 -[46] codetools_0.2-20 affy_1.82.0 miniUI_0.1.1.1 -[49] lattice_0.22-6 tibble_3.2.1 shiny_1.9.1 -[52] withr_3.0.2 evaluate_1.0.1 circlize_0.4.16 -[55] pillar_1.9.0 affyio_1.74.0 BiocManager_1.30.25 -[58] renv_1.0.11 DT_0.33 foreach_1.5.2 -[61] shinyjs_2.1.0 generics_0.1.3 munsell_0.5.1 -[64] scales_1.3.0 xtable_1.8-4 glue_1.8.0 -[67] tools_4.4.2 colourpicker_1.3.0 locfit_1.5-9.10 -[70] colorspace_2.1-1 nlme_3.1-166 GenomeInfoDbData_1.2.12 -[73] vipor_0.4.7 cli_3.6.3 fansi_1.0.6 -[76] viridisLite_0.4.2 S4Arrays_1.4.1 dplyr_1.1.4 -[79] gtable_0.3.6 rintrojs_0.3.4 sass_0.4.9 -[82] digest_0.6.37 SparseArray_1.4.8 ggrepel_0.9.6 -[85] farver_2.1.2 rjson_0.2.23 htmlwidgets_1.6.4 -[88] htmltools_0.5.8.1 lifecycle_1.0.4 shinyWidgets_0.8.7 -[91] httr_1.4.7 GlobalOptions_0.1.2 statmod_1.5.0 -[94] mime_0.12 +[16] promises_1.3.2 shinyAce_0.4.3 UCSC.utils_1.0.0 +[19] preprocessCore_1.66.0 xfun_0.49 cachem_1.1.0 +[22] zlibbioc_1.50.0 jsonlite_1.8.9 listviewer_4.0.0 +[25] later_1.4.1 DelayedArray_0.30.1 BiocParallel_1.38.0 +[28] parallel_4.4.2 cluster_2.1.8 R6_2.5.1 +[31] bslib_0.8.0 limma_3.60.6 jquerylib_0.1.4 +[34] Rcpp_1.0.13-1 iterators_1.0.14 knitr_1.49 +[37] httpuv_1.6.15 Matrix_1.7-1 splines_4.4.2 +[40] igraph_2.1.2 tidyselect_1.2.1 abind_1.4-8 +[43] yaml_2.3.10 doParallel_1.0.17 codetools_0.2-20 +[46] affy_1.82.0 miniUI_0.1.1.1 lattice_0.22-6 +[49] tibble_3.2.1 shiny_1.10.0 withr_3.0.2 +[52] evaluate_1.0.1 circlize_0.4.16 pillar_1.10.0 +[55] affyio_1.74.0 BiocManager_1.30.25 renv_1.0.11 +[58] DT_0.33 foreach_1.5.2 shinyjs_2.1.0 +[61] generics_0.1.3 munsell_0.5.1 scales_1.3.0 +[64] xtable_1.8-4 glue_1.8.0 tools_4.4.2 +[67] colourpicker_1.3.0 locfit_1.5-9.10 colorspace_2.1-1 +[70] nlme_3.1-166 GenomeInfoDbData_1.2.12 vipor_0.4.7 +[73] cli_3.6.3 viridisLite_0.4.2 S4Arrays_1.4.1 +[76] dplyr_1.1.4 gtable_0.3.6 rintrojs_0.3.4 +[79] sass_0.4.9 digest_0.6.37 SparseArray_1.4.8 +[82] ggrepel_0.9.6 farver_2.1.2 rjson_0.2.23 +[85] htmlwidgets_1.6.4 htmltools_0.5.8.1 lifecycle_1.0.4 +[88] shinyWidgets_0.8.7 httr_1.4.7 GlobalOptions_0.1.2 +[91] statmod_1.5.0 mime_0.12
@@ -959,7 +958,7 @@Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/04-exploratory-qc.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/04-exploratory-qc.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/instructor/05-differential-expression.html b/instructor/05-differential-expression.html index 3e016ff5..a66e3f1b 100644 --- a/instructor/05-differential-expression.html +++ b/instructor/05-differential-expression.html @@ -283,7 +283,7 @@Differential expression analysis
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
@@ -1068,7 +1068,7 @@Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/05-differential-expression.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/05-differential-expression.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/instructor/06-extra-design.html b/instructor/06-extra-design.html index ea874605..a58c835d 100644 --- a/instructor/06-extra-design.html +++ b/instructor/06-extra-design.html @@ -285,7 +285,7 @@Extra exploration of design matrices
-Last updated on 2024-12-03 | +
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@@ -648,7 +648,7 @@Challenge
-+R @@ -734,7 +734,7 @@
Challenge
-+R @@ -1981,7 +1981,7 @@
Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/06-extra-design.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/06-extra-design.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/instructor/07-gene-set-analysis.html b/instructor/07-gene-set-analysis.html index c459f298..8aacc2f6 100644 --- a/instructor/07-gene-set-analysis.html +++ b/instructor/07-gene-set-analysis.html @@ -279,7 +279,7 @@Gene set enrichment analysis
-Last updated on 2024-12-03 | +
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@@ -836,9 +836,9 @@ROUTPUT
+ expr min lq mean median uq max neval + fisher 242.642 249.1445 271.24591 252.195 262.1435 1561.651 100 + hyper 1.473 1.7080 2.53325 2.720 2.9710 8.786 100Unit: microseconds - expr min lq mean median uq max neval - fisher 242.563 244.937 262.70772 247.967 251.9505 1406.496 100 - hyper 1.492 1.693 2.33685 2.555 2.8555 6.101 100It is very astonishing that
phyper()is hundreds of times faster thanfisher.test(). Main reason is in @@ -992,7 +992,7 @@Challenge
-+R @@ -1613,7 +1613,7 @@
OUTPUT<
OUTPUT
-
+--> Expected input gene ID: 73884,382007,13214,226356,208188,66197--> Expected input gene ID: 60597,11517,17864,100039030,54486,69496OUTPUT @@ -1890,19 +1890,19 @@
OUTPUT< mmu04913 Ovarian steroidogenesis - Mus musculus (house mouse) mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse) GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue -mmu00590 16/460 89/9818 0.1797753 3.837030 5.960759 3.104291e-06 -mmu00591 12/460 55/9818 0.2181818 4.656759 6.029243 6.756868e-06 -mmu00565 11/460 48/9818 0.2291667 4.891214 5.991495 9.914058e-06 -mmu00592 8/460 25/9818 0.3200000 6.829913 6.470696 1.166851e-05 -mmu04913 12/460 64/9818 0.1875000 4.001902 5.341607 3.445424e-05 -mmu04061 14/460 95/9818 0.1473684 3.145355 4.658408 1.259362e-04 +mmu00590 16/451 89/9569 0.1797753 3.814345 5.932220 3.338144e-06 +mmu00591 12/451 55/9569 0.2181818 4.629228 6.002927 7.161290e-06 +mmu00565 11/451 48/9569 0.2291667 4.862297 5.965873 1.046503e-05 +mmu00592 8/451 25/9569 0.3200000 6.789534 6.446107 1.217181e-05 +mmu04913 12/451 64/9569 0.1875000 3.978243 5.316467 3.643828e-05 +mmu04061 14/451 95/9569 0.1473684 3.126759 4.633002 1.337191e-04 p.adjust qvalue -mmu00590 0.0009101439 0.0007860892 -mmu00591 0.0009101439 0.0007860892 -mmu00565 0.0009101439 0.0007860892 -mmu00592 0.0009101439 0.0007860892 -mmu04913 0.0021499443 0.0018569019 -mmu04061 0.0065486813 0.0056560810 +mmu00590 0.0009494012 0.0008231987 +mmu00591 0.0009494012 0.0008231987 +mmu00565 0.0009494012 0.0008231987 +mmu00592 0.0009494012 0.0008231987 +mmu04913 0.0022737489 0.0019715029 +mmu04061 0.0069533935 0.0060290895 geneID mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687 mmu00591 18783/211429/329502/78390/242546/18781/18784/13113/622127/232889/237625/11687 @@ -2649,7 +2649,7 @@
Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/07-gene-set-analysis.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/07-gene-set-analysis.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/instructor/08-next-steps.html b/instructor/08-next-steps.html index 4add8482..64af17fa 100644 --- a/instructor/08-next-steps.html +++ b/instructor/08-next-steps.html @@ -277,7 +277,7 @@Next steps
-Last updated on 2024-12-03 | +
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@@ -426,7 +426,7 @@Key Points
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/08-next-steps.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/08-next-steps.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html index 260962dc..c9f71bae 100644 --- a/instructor/CODE_OF_CONDUCT.html +++ b/instructor/CODE_OF_CONDUCT.html @@ -265,7 +265,7 @@Contributor Code of Conduct
-Last updated on 2024-12-03 | +
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@@ -342,7 +342,7 @@Contributor Code of Conduct
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/CODE_OF_CONDUCT.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/CODE_OF_CONDUCT.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html index 727f172c..4e44032e 100644 --- a/instructor/LICENSE.html +++ b/instructor/LICENSE.html @@ -265,7 +265,7 @@Licenses
-Last updated on 2024-12-03 | +
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@@ -390,7 +390,7 @@Licenses
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/LICENSE.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/LICENSE.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/instructor/aio.html b/instructor/aio.html index 03adc646..907a1420 100644 --- a/instructor/aio.html +++ b/instructor/aio.html @@ -331,7 +331,7 @@Content from Introduction to RNA-seq
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
Estimated time 100 minutes
@@ -670,7 +670,7 @@Key Points
Content from RStudio Project and Experimental Data
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
Estimated time 30 minutes
@@ -1006,7 +1006,7 @@Key Points
Content from Importing and annotating quantified data into R
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
Estimated time 120 minutes
@@ -1246,7 +1246,7 @@Challenge: Discuss the following points with your neig -
+- In
counts, the rows are genes just like the rows in @@ -1372,7 +1372,7 @@Challenge
-+R @@ -1750,7 +1750,7 @@
Challenge
-+R @@ -1878,7 +1878,7 @@
Challenge: How to subset to mRNA genes
-+R @@ -2075,7 +2075,7 @@
OUTPUT< [13] BiocGenerics_0.50.0 knitr_1.49 loaded via a namespace (and not attached): - [1] Matrix_1.7-1 bit_4.5.0 jsonlite_1.8.9 + [1] Matrix_1.7-1 bit_4.5.0.1 jsonlite_1.8.9 [4] compiler_4.4.2 BiocManager_1.30.25 renv_1.0.11 [7] crayon_1.5.3 blob_1.2.4 Biostrings_2.72.1 [10] png_0.1-8 fastmap_1.2.0 yaml_2.3.10 @@ -2083,7 +2083,7 @@
OUTPUT< [16] S4Arrays_1.4.1 DelayedArray_0.30.1 GenomeInfoDbData_1.2.12 [19] DBI_1.2.3 rlang_1.1.4 KEGGREST_1.44.1 [22] cachem_1.1.0 xfun_0.49 bit64_4.5.2 -[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.8 +[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.9 [28] cli_3.6.3 zlibbioc_1.50.0 grid_4.4.2 [31] vctrs_0.6.5 evaluate_1.0.1 abind_1.4-8 [34] httr_1.4.7 pkgconfig_2.0.3 tools_4.4.2 @@ -2110,7 +2110,7 @@
Key Points
Content from Exploratory analysis and quality control
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
Estimated time 180 minutes
@@ -2717,33 +2717,32 @@OUTPUT< [7] mgcv_1.9-1 png_0.1-8 vctrs_0.6.5 [10] pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3 [13] fastmap_1.2.0 XVector_0.44.0 labeling_0.4.3 -[16] utf8_1.2.4 promises_1.3.2 shinyAce_0.4.3 -[19] UCSC.utils_1.0.0 preprocessCore_1.66.0 xfun_0.49 -[22] cachem_1.1.0 zlibbioc_1.50.0 jsonlite_1.8.9 -[25] listviewer_4.0.0 later_1.4.1 DelayedArray_0.30.1 -[28] BiocParallel_1.38.0 parallel_4.4.2 cluster_2.1.6 -[31] R6_2.5.1 bslib_0.8.0 limma_3.60.6 -[34] jquerylib_0.1.4 Rcpp_1.0.13-1 iterators_1.0.14 -[37] knitr_1.49 httpuv_1.6.15 Matrix_1.7-1 -[40] splines_4.4.2 igraph_2.1.1 tidyselect_1.2.1 -[43] abind_1.4-8 yaml_2.3.10 doParallel_1.0.17 -[46] codetools_0.2-20 affy_1.82.0 miniUI_0.1.1.1 -[49] lattice_0.22-6 tibble_3.2.1 shiny_1.9.1 -[52] withr_3.0.2 evaluate_1.0.1 circlize_0.4.16 -[55] pillar_1.9.0 affyio_1.74.0 BiocManager_1.30.25 -[58] renv_1.0.11 DT_0.33 foreach_1.5.2 -[61] shinyjs_2.1.0 generics_0.1.3 munsell_0.5.1 -[64] scales_1.3.0 xtable_1.8-4 glue_1.8.0 -[67] tools_4.4.2 colourpicker_1.3.0 locfit_1.5-9.10 -[70] colorspace_2.1-1 nlme_3.1-166 GenomeInfoDbData_1.2.12 -[73] vipor_0.4.7 cli_3.6.3 fansi_1.0.6 -[76] viridisLite_0.4.2 S4Arrays_1.4.1 dplyr_1.1.4 -[79] gtable_0.3.6 rintrojs_0.3.4 sass_0.4.9 -[82] digest_0.6.37 SparseArray_1.4.8 ggrepel_0.9.6 -[85] farver_2.1.2 rjson_0.2.23 htmlwidgets_1.6.4 -[88] htmltools_0.5.8.1 lifecycle_1.0.4 shinyWidgets_0.8.7 -[91] httr_1.4.7 GlobalOptions_0.1.2 statmod_1.5.0 -[94] mime_0.12 +[16] promises_1.3.2 shinyAce_0.4.3 UCSC.utils_1.0.0 +[19] preprocessCore_1.66.0 xfun_0.49 cachem_1.1.0 +[22] zlibbioc_1.50.0 jsonlite_1.8.9 listviewer_4.0.0 +[25] later_1.4.1 DelayedArray_0.30.1 BiocParallel_1.38.0 +[28] parallel_4.4.2 cluster_2.1.8 R6_2.5.1 +[31] bslib_0.8.0 limma_3.60.6 jquerylib_0.1.4 +[34] Rcpp_1.0.13-1 iterators_1.0.14 knitr_1.49 +[37] httpuv_1.6.15 Matrix_1.7-1 splines_4.4.2 +[40] igraph_2.1.2 tidyselect_1.2.1 abind_1.4-8 +[43] yaml_2.3.10 doParallel_1.0.17 codetools_0.2-20 +[46] affy_1.82.0 miniUI_0.1.1.1 lattice_0.22-6 +[49] tibble_3.2.1 shiny_1.10.0 withr_3.0.2 +[52] evaluate_1.0.1 circlize_0.4.16 pillar_1.10.0 +[55] affyio_1.74.0 BiocManager_1.30.25 renv_1.0.11 +[58] DT_0.33 foreach_1.5.2 shinyjs_2.1.0 +[61] generics_0.1.3 munsell_0.5.1 scales_1.3.0 +[64] xtable_1.8-4 glue_1.8.0 tools_4.4.2 +[67] colourpicker_1.3.0 locfit_1.5-9.10 colorspace_2.1-1 +[70] nlme_3.1-166 GenomeInfoDbData_1.2.12 vipor_0.4.7 +[73] cli_3.6.3 viridisLite_0.4.2 S4Arrays_1.4.1 +[76] dplyr_1.1.4 gtable_0.3.6 rintrojs_0.3.4 +[79] sass_0.4.9 digest_0.6.37 SparseArray_1.4.8 +[82] ggrepel_0.9.6 farver_2.1.2 rjson_0.2.23 +[85] htmlwidgets_1.6.4 htmltools_0.5.8.1 lifecycle_1.0.4 +[88] shinyWidgets_0.8.7 httr_1.4.7 GlobalOptions_0.1.2 +[91] statmod_1.5.0 mime_0.12
@@ -2766,7 +2765,7 @@Key Points
Content from Differential expression analysis
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
Estimated time 105 minutes
@@ -3522,7 +3521,7 @@Key Points
Content from Extra exploration of design matrices
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
Estimated time 60 minutes
@@ -3886,7 +3885,7 @@Challenge
-+R @@ -3973,7 +3972,7 @@
Challenge
-+R @@ -5185,7 +5184,7 @@
Key Points
Content from Gene set enrichment analysis
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
Estimated time 105 minutes
@@ -5782,9 +5781,9 @@ROUTPUT
+ expr min lq mean median uq max neval + fisher 242.642 249.1445 271.24591 252.195 262.1435 1561.651 100 + hyper 1.473 1.7080 2.53325 2.720 2.9710 8.786 100Unit: microseconds - expr min lq mean median uq max neval - fisher 242.563 244.937 262.70772 247.967 251.9505 1406.496 100 - hyper 1.492 1.693 2.33685 2.555 2.8555 6.101 100It is very astonishing that
phyper()is hundreds of times faster thanfisher.test(). Main reason is in @@ -5942,7 +5941,7 @@Challenge
-+R @@ -6599,7 +6598,7 @@
OUTPUT<
OUTPUT
-
+--> Expected input gene ID: 73884,382007,13214,226356,208188,66197--> Expected input gene ID: 60597,11517,17864,100039030,54486,69496OUTPUT @@ -6883,19 +6882,19 @@
OUTPUT< mmu04913 Ovarian steroidogenesis - Mus musculus (house mouse) mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse) GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue -mmu00590 16/460 89/9818 0.1797753 3.837030 5.960759 3.104291e-06 -mmu00591 12/460 55/9818 0.2181818 4.656759 6.029243 6.756868e-06 -mmu00565 11/460 48/9818 0.2291667 4.891214 5.991495 9.914058e-06 -mmu00592 8/460 25/9818 0.3200000 6.829913 6.470696 1.166851e-05 -mmu04913 12/460 64/9818 0.1875000 4.001902 5.341607 3.445424e-05 -mmu04061 14/460 95/9818 0.1473684 3.145355 4.658408 1.259362e-04 +mmu00590 16/451 89/9569 0.1797753 3.814345 5.932220 3.338144e-06 +mmu00591 12/451 55/9569 0.2181818 4.629228 6.002927 7.161290e-06 +mmu00565 11/451 48/9569 0.2291667 4.862297 5.965873 1.046503e-05 +mmu00592 8/451 25/9569 0.3200000 6.789534 6.446107 1.217181e-05 +mmu04913 12/451 64/9569 0.1875000 3.978243 5.316467 3.643828e-05 +mmu04061 14/451 95/9569 0.1473684 3.126759 4.633002 1.337191e-04 p.adjust qvalue -mmu00590 0.0009101439 0.0007860892 -mmu00591 0.0009101439 0.0007860892 -mmu00565 0.0009101439 0.0007860892 -mmu00592 0.0009101439 0.0007860892 -mmu04913 0.0021499443 0.0018569019 -mmu04061 0.0065486813 0.0056560810 +mmu00590 0.0009494012 0.0008231987 +mmu00591 0.0009494012 0.0008231987 +mmu00565 0.0009494012 0.0008231987 +mmu00592 0.0009494012 0.0008231987 +mmu04913 0.0022737489 0.0019715029 +mmu04061 0.0069533935 0.0060290895 geneID mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687 mmu00591 18783/211429/329502/78390/242546/18781/18784/13113/622127/232889/237625/11687 @@ -7618,7 +7617,7 @@
Key Points
Content from Next steps
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
Estimated time 20 minutes
diff --git a/instructor/discuss.html b/instructor/discuss.html index 6d621c24..e6a61a9b 100644 --- a/instructor/discuss.html +++ b/instructor/discuss.html @@ -265,7 +265,7 @@Discussion
-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
@@ -335,7 +335,7 @@Discussion
"url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/discuss.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/discuss.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/instructor/reference.html b/instructor/reference.html index 9a3f6e97..6b69585e 100644 --- a/instructor/reference.html +++ b/instructor/reference.html @@ -265,7 +265,7 @@-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
@@ -334,7 +334,7 @@ "url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/reference.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/reference.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" } diff --git a/md5sum.txt b/md5sum.txt index df098712..40573f87 100644 --- a/md5sum.txt +++ b/md5sum.txt @@ -1,19 +1,19 @@ "file" "checksum" "built" "date" -"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2024-12-03" -"LICENSE.md" "2fb7308e51efc6894f5fb9794505973e" "site/built/LICENSE.md" "2024-12-03" -"config.yaml" "6145f67cb03c9875f6ec5b6417a330eb" "site/built/config.yaml" "2024-12-03" -"index.md" "6a1b0b9e8983481699e2e4ef54a4893a" "site/built/index.md" "2024-12-03" -"episodes/01-intro-to-rnaseq.Rmd" "b4d2d36be5042834578061b30665d493" "site/built/01-intro-to-rnaseq.md" "2024-12-03" -"episodes/02-setup.Rmd" "e62af0b59eec704194484af83db5b859" "site/built/02-setup.md" "2024-12-03" -"episodes/03-import-annotate.Rmd" "c43d8eab0fcc982993ea35a952d323c0" "site/built/03-import-annotate.md" "2024-12-03" -"episodes/04-exploratory-qc.Rmd" "af033b6158f06de3f33d41673272a87d" "site/built/04-exploratory-qc.md" "2024-12-03" -"episodes/05-differential-expression.Rmd" "29ab3939367a0b3521cfd764929e3aee" "site/built/05-differential-expression.md" "2024-12-03" -"episodes/06-extra-design.Rmd" "e4859b8e76bc6d0c8d5c598e1d00b37b" "site/built/06-extra-design.md" "2024-12-03" -"episodes/07-gene-set-analysis.Rmd" "e7b69b6f2af11dfab883303e9a50981d" "site/built/07-gene-set-analysis.md" "2024-12-03" -"episodes/08-next-steps.Rmd" "88227f8b7b9ae91bd86a66a93d722946" "site/built/08-next-steps.md" "2024-12-03" -"instructors/instructor-notes.md" "a59fd3b94c07c3fe3218c054a0f03277" "site/built/instructor-notes.md" "2024-12-03" -"learners/discuss.md" "2758e2e5abd231d82d25c6453d8abbc6" "site/built/discuss.md" "2024-12-03" -"learners/reference.md" "b9aea3dd8169bf1105bf4f462e8e38f5" "site/built/reference.md" "2024-12-03" -"learners/setup.md" "29d12719c4fcebc031f726275706b330" "site/built/setup.md" "2024-12-03" -"profiles/learner-profiles.md" "28ba7f4d04639862db131119f4dc4f4d" "site/built/learner-profiles.md" "2024-12-03" -"renv/profiles/lesson-requirements/renv.lock" "dab1d5b60ee11358b891d79a83d474d8" "site/built/renv.lock" "2024-12-03" +"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2025-01-07" +"LICENSE.md" "2fb7308e51efc6894f5fb9794505973e" "site/built/LICENSE.md" "2025-01-07" +"config.yaml" "6145f67cb03c9875f6ec5b6417a330eb" "site/built/config.yaml" "2025-01-07" +"index.md" "6a1b0b9e8983481699e2e4ef54a4893a" "site/built/index.md" "2025-01-07" +"episodes/01-intro-to-rnaseq.Rmd" "b4d2d36be5042834578061b30665d493" "site/built/01-intro-to-rnaseq.md" "2025-01-07" +"episodes/02-setup.Rmd" "e62af0b59eec704194484af83db5b859" "site/built/02-setup.md" "2025-01-07" +"episodes/03-import-annotate.Rmd" "c43d8eab0fcc982993ea35a952d323c0" "site/built/03-import-annotate.md" "2025-01-07" +"episodes/04-exploratory-qc.Rmd" "af033b6158f06de3f33d41673272a87d" "site/built/04-exploratory-qc.md" "2025-01-07" +"episodes/05-differential-expression.Rmd" "29ab3939367a0b3521cfd764929e3aee" "site/built/05-differential-expression.md" "2025-01-07" +"episodes/06-extra-design.Rmd" "e4859b8e76bc6d0c8d5c598e1d00b37b" "site/built/06-extra-design.md" "2025-01-07" +"episodes/07-gene-set-analysis.Rmd" "e7b69b6f2af11dfab883303e9a50981d" "site/built/07-gene-set-analysis.md" "2025-01-07" +"episodes/08-next-steps.Rmd" "88227f8b7b9ae91bd86a66a93d722946" "site/built/08-next-steps.md" "2025-01-07" +"instructors/instructor-notes.md" "a59fd3b94c07c3fe3218c054a0f03277" "site/built/instructor-notes.md" "2025-01-07" +"learners/discuss.md" "2758e2e5abd231d82d25c6453d8abbc6" "site/built/discuss.md" "2025-01-07" +"learners/reference.md" "b9aea3dd8169bf1105bf4f462e8e38f5" "site/built/reference.md" "2025-01-07" +"learners/setup.md" "29d12719c4fcebc031f726275706b330" "site/built/setup.md" "2025-01-07" +"profiles/learner-profiles.md" "28ba7f4d04639862db131119f4dc4f4d" "site/built/learner-profiles.md" "2025-01-07" +"renv/profiles/lesson-requirements/renv.lock" "1b6609e44b4f4efe3cb2376d1a60a6b6" "site/built/renv.lock" "2025-01-07" diff --git a/pkgdown.yml b/pkgdown.yml index 43c8bf73..668380b3 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,4 +2,4 @@ pandoc: 3.1.11 pkgdown: 2.1.1 pkgdown_sha: ~ articles: {} -last_built: 2025-01-07T00:54Z +last_built: 2025-01-07T07:51Z diff --git a/reference.html b/reference.html index ef2c1262..642d3855 100644 --- a/reference.html +++ b/reference.html @@ -265,7 +265,7 @@-Last updated on 2024-12-03 | +
Last updated on 2025-01-07 | Edit this page
@@ -332,7 +332,7 @@ "url": "https://carpentries-incubator.github.io/bioc-rnaseq/reference.html", "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/reference.html", "dateCreated": "2020-09-15", - "dateModified": "2024-12-03", + "dateModified": "2025-01-07", "datePublished": "2025-01-07" }
- In
- In
- In