[Bioc-devel] Deprecated Packages for upcoming Release 3.23

[Kern, Lori]

For current running list of deprecated package for the current release and devel versions of Bioconductor, you can also refer to https://bioconductor.org/developers/help_wanted/#deprecated-packages

This page is updated automatically throughout the year.


Lori Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Kern, Lori via Bioc-devel <bioc-devel using r-project.org>
Sent: Monday, April 13, 2026 9:07 AM
To: Holger Schwender via Bioc-devel <bioc-devel using r-project.org>
Subject: [Bioc-devel] Deprecated Packages for upcoming Release 3.23

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. This is the current list of deprecated packages for Bioc 3.23.
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 using r-project.org mailing list
Do not un-deprecate a package yourself. You must request un-deprecation from the Bioconductor core team at bioc-devel using r-project.org. We will not recognize self un-deprecation.
Software:
BubbleTree
CuratedAtlasQueryR
IONiseR
hmdbQuery
rols
scviR
SGCP
APAlyzer
ballgown
bamsignals
barcodetrackR
basecallQC
biobroom
biodbChebi
BiRewire
BPRMeth
CelliD
ChIPQC
ccrepe
cummeRbund
debCAM
DeconRNASeq
geneXtendeR
GEOexplorer
GNET2
granulator
hca
IMAS
Melissa
MetaNeighbor
MethReg
mfa
microSTASIS
MineICA
motifcounter
MSPrep
nearBynding
netprioR
normr
Organism.dplyr
partCNV
RcisTarget
receptLoss
RgnTX
RiboProfiling
RTCGA
shiny.gosling
soGGi
SigFuge
spatzie
SQLDataFrame
supersigs
tLOH

ExperimentData:
curatedBreastData
Fletcher2013b
rRDPData

AnnotationData:
hpAnnot


Lori Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://secure-web.cisco.com/1OY0Xxzgpg4q-lgMKTxK9hSy6heFAWEVSJ5xf6pqY3FA1mNat8g31ejU-iWBBQ2Vm62kYGl_G0wSKCDOSBp7UfAKwzzX5DTU7yCxohx8h0i8cxTVxkb2MJcbD03PR7nu0_0UzQOCptLUxfu32SE9iPMIqPcRUpDzSu-2V0GyaCQ3thXVdag27tRHHT-c1OEczGez6sPGPqz5xhtKe9lkXl9lr4m2HuG2Au2sgGd31PXxS9WM_m7R9a_Gl39ytdEdcZoITnDKmSqdoKI0Ciu6eHKozGhp4ZjP91ZyFcDEsZCy8l-05VB0G_lInrrE4OQmwTrrw4_bmnmTq2KttKBrOoQ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel



This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]