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 3.11 is as follows:

Maintainer requested deprecation:

• Software:

  • QUALIFIER
  • motifRG
  • triform

• Annotation:

  • org.At.tair.db
  • hom.At.inp.db
  • hom.Ce.inp.db
  • hom.Dm.inp.db
  • hom.Dr.inp.db
  • hom.Hs.inp.db
  • hom.Mm.inp.db
  • hom.Rn.inp.db
  • hom.Sc.inp.db
  • KEGG.db (use KEGGREST instead)

Unresponsive/not-maintained packages:

• Software:

  • SELEX
  • CTDquerier

The follow Annotation packages were deprecated in 3.10 and removed from 3.11 but not previously announced.

• MafDb.ESP6500SI.V2.SSA137.hs37d5
• MafDb.EXP6500SI.V2.SSA137.GRCh38

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