[Bioc-devel] List of Deprecated Packages Bioconductor 3.13

[Kern, Lori]

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 3.13 :

Maintainer requested deprecation:

Software:

BiocCaseStudies
HCABrowser
HCAExplorer
HCAMatrixBrowse
ChIPSeqSpike
MSEADbi
RchyOptimyx
RNAither
SAGx
yaqcaffy

Experiment Data:

ceu1kg
ceu1kgv
ceuhm3
cgdv17
dsQTL
hmyriB36
yri1kgv


Workflow:

eQTL


Unresponsive/not-maintained packages:

Software:

AffyExpress
affyQCReport
AnnotationFuncs
ArrayTools
bigmemoryExtras
CancerMutationAnalysis
CexoR
CrossICC
CoRegFlux
cytofast
DBChIP
dexus
EasyqpcR
EDDA
eisa
ELBOW
ExpressionView
genoset
Imetagene
IntramiRExploreR
mdgsa
methyAnalysis
OutlierD
pcot2
PCpheno
Polyfit
POST
RDAVIDWebService
RNAprobR
rnaSeqMap
samExploreR
seqplots
simulatorZ
SSPA


Experiment Data:

facsDorit
gskb
JctSeqData
plasFIA

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.

Previously listed as deprecated but have been undeprecated:

ExperimentData

DmelSGI
RNAinteractMAPK
sampleClassifierData
plasFia

Software

APAlyzer
metagene2
proFia
sampleClassifier
sojourner



Cheers,




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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