12.2 R contrib

All other packages:

• CRAN: Comprehensive R Archive Network
  • 15356^* packages available
  • find packages in https://cran.r-project.org/web/packages/
• Bioconductor:
  • 1823^* packages available
  • find packages in https://bioconductor.org/packages

As of February 2019*

Bioconductor

Set of R packages specialized in the analysis of bioinformatics data.

Bioconductor supports most types of genomics and NGS data (e.g. limma, DESeq2, BayesPeak) and integrates:

• Specific data classes (e.g. Granges from GenomicRanges)
• Integrates command line tools (e.g Rsamtools)
• Annotation tools (e.g. biomaRt)

There are different types of Bioconductor packages:

• Software: set of functions
  • e.g. DESeq2 (NGS data analysis)
• Annotation: annotation of specific arrays, organisms, events, etc.
  • e.g. BSgenome.Hsapiens.UCSC.hg38
• Experiment: data that can be loaded and used
  • e.g. ALL (acute lymphoblastic leukemia dataset)