The Bioconductor Team has identified the following list of deprecated packages:

Maintainer requested deprecation:

Software Package:

ontoCAT

spliceR (functionalities moved to IsoformSwitchAnalyzeR)

mvGST

Experiment Data Package:

RnaSeqTutorial

cheung2010

MEALData (replaced with brgedata)

Unresponsive/not-maintained packages:

Software:

GMRP

MBttest

OperaMate

DASC

htSeqTools

PAnnBuilder

DMRScan

phenoDist

We did not announce that the following is also no longer available Experiment Data Package: IlluminaHumanMethylation450k.db

BrowserVizDemo  has also requested deprecation.