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. This is the current list of deprecated packages for Bioc 3.12 :

Maintainer requested deprecation:

• Software:

  • CGEN
  • DESeq : See replacement DESeq2
  • chimera
  • explorase
  • flowFit
  • flowSpy
  • GGBase
  • GGtools
  • netReg
  • mcaGUI
  • metaseqR : See replacement metaseqR2
  • MOFA
  • NarrowPeaks
  • OGSA
  • PGA
  • prada
  • rTANDEM
  • sapFinder
  • scsR
  • shinyTANDEM
  • simpleaffy
  • spotSegmentation
  • xps

• Experiment Data:

  • GGdata
  • flowFitExampleData

Unresponsive/not-maintained packages:

• Software:

  • adaptest
  • ArrayTV
  • BioSeqClass
  • CHARGE
  • CNVtools
  • CorMut
  • flowType
  • flowVS
  • focalCall
  • FourCSeq
  • FunciSNP
  • GenRank
  • GeneticsDesign
  • GOFunction
  • hicrep
  • ImpulseDE
  • ImpulseDE2
  • joda
  • JunctionSeq
  • LINC
  • Logolas
  • methVisual
  • methyvim
  • Mirsynergy
  • MmPalateMiRNA
  • MotIV
  • netbenchmark
  • OmicsMarkeR
  • pathprint
  • PathwaySplice
  • PGSEA
  • plrs
  • Prize
  • Rariant
  • reb
  • Roleswitch
  • sampleClassifier
  • sigaR
  • signet
  • Starr
  • SVAPLSeq

• ExpermentData:

  • FunciSNP.data
  • mitoODEdata
  • Mulder2012
  • RNAinteractMAPK
  • methyvimData
  • pathprintGEOData
  • sampleClassiferData

It should be noted, we did try to reach out to these package maintainers multiple times and they were either unresponsive or had emails bounce. We encourage anyone that is familiar with a package maintainer on this list to reach out to them and notify them directly. Packages can be un-deprecated if a maintainer fixes the package to build/check cleanly before the next release and requests un-deprecation on the bioc-devel@r-project.org mailing list.

The following packages were previously announced as deprecated but had maintainers reach back out to fix the package. The packages are undeprecated and will remain in Bioconductor:

• BioNet
• MFPE
• MAIT
• safe
• omicade4
• GeneOverlap
• gage
• NOISeq
• omicRexposome
• PWMEnrich
• PWMEnrich.Dmelanogaster.background
• PWMEnrich.Hsapiens.background
• PWMEnrich.Mmusculus.background

The follow have responded and will be un-deprectated

Software:

• made4

Experiment Data:

• RnaSeqSampleSizeData

The follow are additional deprecations:

User-requested:

ExperimentPackages:

• geuvStore2
• geuvPack
• yriMulti

Software packages:

• gQTLBase
• gQTLstats
• TxRegInfra

Unresponsive These are accompanied software or experiment data packages of unresponsive maintainers whose packages were already deprecated or being deprecated this release:

• pcaGoPromoter.Hs.hg19
• pcaGoPromoter.Mm.mm9
• pcaGoPromoter.Rn.rn4
• waveTilingData

metaArray has also requested deprecation