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NEWS.md

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seeker 1.1.6

  • Made error handling more graceful.

seeker 1.1.5

  • Added support for GPL17811 (thanks to @jacorvar).

seeker 1.1.4

  • Fixed processing of ArrayExpress data (thanks to @jacorvar).
  • Removed deprecated argument from biomaRt::listEnsemblArchives().

seeker 1.1.3

  • Updated test for fetching metadata again.
  • fetchMetadata() now orders its result.

seeker 1.1.2

  • Updated test for fetching metadata.

seeker 1.1.1

  • Updated test expectations for altered column order in metadata from ENA.

seeker 1.1.0

  • Removed dependency on ArrayExpress package.

seeker 1.0.14

  • Fixed handling of whitespace in file paths while installing miniconda.

seeker 1.0.13

  • Updated for BioStudies API.

seeker 1.0.12

  • fetchMetadata() can now save the metadata to a text file.

seeker 1.0.11

  • Revised documentation.

seeker 1.0.10

  • Revised package for CRAN.

seeker 1.0.9

  • Revised "Description" text.y
  • Skipped more tests on CRAN to avoid installation of packages.

seeker 1.0.8

  • Removed default install directories for dependencies in installSysDeps().
  • Replaced options(warn=-1) to use suppressWarnings().
  • Updated description text.
  • Revised console printing.

seeker 1.0.7

  • Added support for more platforms.
  • Added ability for seekerArray() to skip processing the expression data.

seeker 1.0.6

  • Added installation of snakemake by installSysDeps() for easier reproducible analyses.

seeker 1.0.5

  • Added argument to installSysDeps() to specify directory in which to create or modify .Rprofile.

seeker 1.0.4

  • Skipped "getNaiveEsetAe() supported" test on CRAN due to BioConductor issues.

seeker 1.0.3

  • Made getProbeGeneMapping() test check for version number of mapping package.
  • Revised arguments for seekerArray() and updated tests and vignettes accordingly.

seeker 1.0.2

  • Set default parent directory for seekerArray().
  • Added custom CDF support for platform GPL17400.

seeker 1.0.1

  • Updated seeker() to save unmodified metadata file.

seeker 1.0.0

  • Updated seeker() to output info of SRA Toolkit-based dependencies.
  • Revised tests and updated version number to prepare for a CRAN submission.

seeker 0.0.0.9068

  • Updated run_seeker.sh to use correct conda environment.
  • Updated Reproducibility vignette to not require local installation of the R package.

seeker 0.0.0.9067

  • Changed species to organism for consistency with NCBI and other packages.
  • Added checking for parallel backend.

seeker 0.0.0.9062

  • Fixed syntax to adhere to lab code style.