update README.md

README.md

@@ -1,6 +1,6 @@
 ## yeastDrop-Seq Computational Pipeline
 
-This repository contains scripts for data pre-processing and downstream analysis in the [yeastDrop-Seq paper].
+This repository contains scripts for data pre-processing and downstream analysis in the [yeastDrop-Seq paper](#).
 
 ### Required softwares
 
@@ -11,3 +11,19 @@ This repository contains scripts for data pre-processing and downstream analysis
 [STAR](https://github.com/alexdobin/STAR)
 [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic)
 [subread](http://subread.sourceforge.net/)
+
+#### Downstream analysis
+[SC3](https://bioconductor.org/packages/release/bioc/html/SC3.html)
+[SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html)
+[Seurat](https://cran.r-project.org/web/packages/Seurat/index.html)
+[ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html)
+[scales](https://cran.r-project.org/web/packages/scales/index.html)
+[ggpubr](https://cran.r-project.org/web/packages/ggpubr/index.html)
+[cowplot](https://cran.r-project.org/web/packages/cowplot/index.html)
+[RColorBrewer](https://cran.r-project.org/web/packages/RColorBrewer/)
+[networkD3](https://cran.r-project.org/web/packages/networkD3/index.html)
+[dplyr](https://cran.r-project.org/web/packages/dplyr/index.html)
+[patchwork](https://cran.r-project.org/web/packages/patchwork/)
+[reshape2](https://cran.r-project.org/web/packages/reshape2/index.html)
+[clusterProfiler](https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html)
+[org.Sc.sgd.db](https://bioconductor.org/packages/release/data/annotation/html/org.Sc.sgd.db.html)

in_house_scripts/wrapper.R

@@ -11,7 +11,6 @@ require(RColorBrewer)
 require(networkD3)
 require(dplyr)
 require(patchwork)
-require(WebGestaltR)
 library(reshape2)
 library(clusterProfiler)
 library(org.Sc.sgd.db)