The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The current list of deprecated packages for Bioc 3.10 is as follows:

Maintainer requested deprecation:

• Software:

  • SNPchip
  • GenomeGraphs
  • GSEAlm
  • HTSanalyzeR
  • Rchemcpp
  • charm

• Experiment Data Package:

  • charmData

Unresponsive/not-maintained packages:

• Software:

  • digit
  • dSimer
  • flipflop
  • exomePeak
  • CNPBayes
  • brainImageR
  • plateCore
  • rHVDM
  • SEPA
  • seqplots
  • viper

• Experiment Data Package:

  • facopy.annot
  • diggitdata

We will be sending emails out to packages that have been broken across all platforms for an extended period of time as those are packages that are up for immediate deprecation if not corrected in a timely fashion. Thank you

Two Annotation Packages have been user requested deprecated:

• MafDb.gnomADex.r2.0.1.GRCh38
• MafDb.gnomAD.r2.0.1.GRCh38

They are replaced with

• MafDb.gnomADex.r2.1.GRCh38
• MafDb.gnomAD.r2.1.GRCh38

Unmentioned previously the following Annotation Packages have also been deprecated:

• MafDb.gnomADex.r2.0.1.hs37d5
• MafDb.gnomAD.r2.0.1.hs37d5

They are replaced with

• MafDb.gnomADex.r2.1.hs37d5
• MafDb.gnomAD.r2.1.hs37d5