April 27, 2022

Bioconductors:

We are pleased to announce Bioconductor 3.15, consisting of 2140 software packages, 410 experiment data packages, 909 annotation packages, 29 workflows and 8 books.

There are 78 new software packages, 5 new data experiment packages, 8 new annotation packages, no new workflows, no new books, and many updates and improvements to existing packages.

Bioconductor 3.15 is compatible with R 4.2.0, and is supported on Linux, 64-bit Windows, and Intel 64-bit macOS 10.13 (High Sierra) or higher. We do not currently support arm64 so arm64 Mac users who wish to install Bioconductor Mac binary packages must install the Intel 64-bit build of R available on CRAN. This release will include updated Bioconductor Docker containers.

Thank you to everyone for your contribution to Bioconductor

Visit Bioconductor BiocViews for details and downloads.

Contents

Getting Started with Bioconductor 3.15

To update to or install Bioconductor 3.15:

  1. Install R 4.2.0. Bioconductor 3.15 has been designed expressly for this version of R.

  2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 78 new software packages in this release of Bioconductor.

New Data Experiment Packages

There are 5 new data experiment packages in this release of Bioconductor.

New Annotation Packages

There are 8 new annotation packages in this release of Bioconductor.

New Workflow Packages

There are no new workflow packages.

New Books

There are no new online books.

NEWS from new and existing Software Packages

ADaCGH2

             Changes in version 2.35.1 (2022-04-19)                 

affxparser

             Changes in version 1.67.1 (2022-03-23)                 

SIGNIFICANT CHANGES

SOFTWARE QUALITY

airpart

                    Changes in version 1.3.4                        

alevinQC

                   Changes in version 1.11.1                        

AlpsNMR

             Changes in version 3.5.1 (2022-04-07)                  

AnnotationHub

                    Changes in version 3.3.0                        

NEW FEATURES

USER-VISIBLE MODIFICATIONS

BUG CORRECTION

AnnotationHubData

                   Changes in version 1.25.0                        

SIGNIFICANT UPDATES

NEW FEATURES

MODIFICATIONS

AnVIL

                    Changes in version 1.8.0                        

NEW FEATURES

USER VISIBLE CHANGES

BUG FIXES

BUG FIXES

BUG FIXES

APAlyzer

             Changes in version 1.9.4 (2022-02-28)                  

aroma.light

             Changes in version 3.25.1 (2022-04-21)                 

BUG FIXES

ATACseqQC

                   Changes in version 1.19.3                        

atena

             Changes in version 1.2.0 (2022-04-21)                  

USER VISIBLE CHANGES

AUCell

                    Changes in version 1.17                         

BANDITS

                   Changes in version 1.11.1                        

bandle

                   Changes in version 1.0.0                       

version 0.99.8

version 0.99.7

version 0.99.6

version 0.99.5

version 0.99.4

version 0.99.2

version 0.0

BASiCS

             Changes in version 2.7.1 (2021-11-03)                  

BayesSpace

                    Changes in version 1.5.1                        

Minor improvements and fixes

New Bioconductor devel (3.15)

BEclear

             Changes in version 2.11.1 (2022-03-31)                 

beer

             Changes in version 0.99.8 (2022-02-14)                 

benchdamic

             Changes in version 1.1.1 (2021-03-21)                  

BindingSiteFinder

                    Changes in version 1.1.2                        

bioCancer

                   Changes in version 1.23.03                       

BiocCheck

                    Changes in version 1.32                         

NEW FEATURES

BUG FIXES AND MINOR IMPROVEMENTS

BiocFileCache

                     Changes in version 2.3                         

ENHANCEMENT

BioCor

                   Changes in version 1.19.1                        

BiocParallel

                    Changes in version 1.30                         

USER VISIBLE CHANGES

BUG FIXES

BiocStyle

                   Changes in version 2.24.0                        

BUG FIXES

biocViews

                   Changes in version 1.63.0                        

BUG FIX

biodb

             Changes in version 1.3.3 (2022-04-02)                  

biodbChebi

             Changes in version 1.1.1 (2022-03-15)                  

biodbExpasy

             Changes in version 0.99.0 (2022-03-15)                 

biodbHmdb

             Changes in version 1.1.2 (2022-03-13)                  

biodbKegg

             Changes in version 1.1.1 (2022-03-17)                  

biodbLipidmaps

             Changes in version 1.1.1 (2022-03-17)                  

biodbMirbase

             Changes in version 0.99.1 (2022-04-01)                 

biodbNcbi

             Changes in version 0.99.6 (2022-03-24)                 

biodbNci

             Changes in version 0.99.0 (2022-03-22)                 

biodbUniprot

             Changes in version 1.1.1 (2022-03-17)                  

biomaRt

                   Changes in version 2.52.0                        

BUG FIXES

BiRewire

                   Changes in version 3.27.5                        

BridgeDbR

                    Changes in version 2.5.0                        

NEW FEATURES

BUG FIXES

bugsigdbr

                    Changes in version 1.2.0                        

CAGEr

                    Changes in version 2.2.0                        

BUG FIXES

CAMERA

                   Changes in version 1.51.1                        

USER VISIBLE CHANGES

canceR

                   Changes in version 1.29.03                       

cbaf

             Changes in version 1.18.0 (2022-04-24)                 

New Features

CBEA

                   Changes in version 0.99.3                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

None

                   Changes in version 0.99.2                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

None

                   Changes in version 0.99.1                        

NEW FEATURES

None

SIGNIFICANT USER-VISIBLE CHANGES

None

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

None

BUG FIXES

None

cBioPortalData

                    Changes in version 2.8.0                        

New features

Bug fixes and minor improvements

cbpManager

                    Changes in version 1.3.2                        

celda

             Changes in version 1.11.0 (2022-03-31)                 

ceRNAnetsim

             Changes in version 1.7.3 (2022-15-03)                  

ChIPpeakAnno

                   Changes in version 3.29.6                        

ChIPQC

                   Changes in version 1.31.2                        

ChIPseeker

                   Changes in version 1.32.2                        

chromstaR

                   Changes in version 1.21.1                        

BUG FIXES

CIMICE

                    Changes in version 1.3.1                        

Overview:

ClassifyR

                    Changes in version 3.0.0                        

cleanUpdTSeq

                   Changes in version 1.33.2                        

clusterProfiler

                    Changes in version 4.3.4                        

clustifyr

             Changes in version 1.7.3 (2022-03-09)                  

CNVMetrics

                    Changes in version 0.1.6                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

cola

                    Changes in version 2.1.1                        

coMET

             Changes in version 1.27.2 (2022-04-18)                 

coMethDMR

                   Changes in version 0.99.9                        

We have been working on bug fixes and formatting/documentation changes as requested during the Bioconductor review. See these requests here: https://github.com/Bioconductor/Contributions/issues/2064

Breaking Changes

Major Changes

Bolstered documentation across all package help / manual files

Bug Fixes

                   Changes in version 0.99.1                        

Migrated all clean files to this repository. All development history in https://github.com/TransBioInfoLab/coMethDMR_old

                 Changes in version 0.0.0.9001                      

Major Changes

Included EPIC arrays annotation (#1) Added a check that: (#5) The rownames of the beta matrix are probe IDs, and There are only numeric columns in the beta matrix

Bug Fixes

compcodeR

                   Changes in version 1.31.1                        

ComplexHeatmap

                   Changes in version 2.11.1                        

CompoundDb

                    Changes in version 0.99                         

Changes in version 0.99.12

Changes in version 0.99.11

Changes in version 0.99.10

Changes in version 0.99.9

Changes in version 0.99.8

Changes in version 0.99.7

Changes in version 0.99.6

Changes in version 0.99.5

Changes in version 0.99.4

Changes in version 0.99.3

Changes in version 0.99.2

Changes in version 0.99.1

Changes in version 0.99.0

Changes in version 0.9.4

Changes in version 0.9.3

Changes in version 0.9.2

Changes in version 0.9.1

Changes in version 0.9.0

Changes in version 0.8.1

Changes in version 0.8.0

Changes in version 0.7.0

Changes in version 0.6.6

Changes in version 0.6.5

Changes in version 0.6.4

Changes in version 0.6.3

Changes in version 0.6.2

Changes in version 0.6.1

Changes in version 0.6.0

Changes in version 0.5.0

Changes in version 0.4.3

Changes in version 0.4.2

Changes in version 0.4.0

Changes in version 0.3.2

Changes in version 0.3.1

Changes in version 0.3.0

Changes in version 0.2.3

Changes in version 0.2.2

Changes in version 0.2.1

Changes in version 0.2.0

Changes in version 0.1.1

Changes in version 0.1.0

conclus

             Changes in version 1.3.4 (2022-03-28)                  

CoreGx

                    Changes in version 2.0.0                        

COTAN

                   Changes in version 0.99.12                       

Release before the official release of Bioc 3.15. Main changes:

Initial Bioconductor release

crisprBase

                    Changes in version 1.0.0                        

crisprBowtie

                    Changes in version 1.0.0                        

crisprScore

                    Changes in version 1.0.0                        

csdR

                    Changes in version 1.1.3                        

Added citation to the csdR article which is now printed.

                    Changes in version 1.1.2                        

Made it explicit in the documentation that missing values are not allows and wrote a test for this case.

                    Changes in version 1.1.1                        

Made some minor modifications to the README and the vignette.

customCMPdb

             Changes in version 1.5.1 (2022-01-31)                  

cytomapper

             Changes in version 1.7.2 (2022-04-20)                  

cytoMEM

             Changes in version 0.99.2 (2022-04-11)                 

CytoML

                    Changes in version 3.11                         

API Changes

Fixes/internal changes

API Changes

Fixes/internal changes

dasper

                    Changes in version 1.5.1                        

NEW FEATURES

dce

             Changes in version 1.3.5 (2022-04-14)                  

dearseq

             Changes in version 1.7.2 (2022-04-13)                  

decoupleR

                     Changes in version 2.2                         

Changes

Changes

New features

Bugfixes

deepSNV

             Changes in version 1.99.3 (2013-07-25)                 

Updates

Bugfixes

Updates

Bugfixes

Updates

Bugfixes

Updates

DEGreport

                   Changes in version 1.31.6                        

DelayedArray

                   Changes in version 0.22.0                        

DEPRECATED AND DEFUNCT

BUG FIXES

DepecheR

                   Changes in version 1.11.4                        

DepInfeR

             Changes in version 0.99.7 (2022-04-05)                 

DEWSeq

             Changes in version 1.9.2 (2022-04-19)                  

DExMA

                    Changes in version 1.3.1                        

DiffBind

                     Changes in version 3.6                         

distinct

                    Changes in version 1.7.2                        

dittoSeq

                     Changes in version 1.8                         

DMRcate

                    Changes in version 2.8.1                        

DOSE

                   Changes in version 3.21.2                        

edgeR

                   Changes in version 3.38.0                        

enrichplot

                   Changes in version 1.15.4                        

ensembldb

                   Changes in version 2.19.10                       

ensemblVEP

                   Changes in version 1.37.0                        

epialleleR

             Changes in version 1.3.6 (2022-02-16)                  

EpiCompare

                 Changes in version 0.99.3

New Features

New features

New Features

epigraHMM

                    Changes in version 1.3.2                        

epimutacions

                   Changes in version 0.99.33                       

escape

                    Changes in version 1.4.1                        

EWCE

                    Changes in version 1.3.3                        

New features

Bug fixes

New features

exomePeak2

             Changes in version 1.7.0 (2022-04-20)                  

ExperimentHub

                    Changes in version 2.3.0                        

USER VISIBLE MODIFICATIONS

ExperimentHubData

                   Changes in version 1.21.0                        

MODIFICATIONS

fastreeR

                    Changes in version 1.0.0                        

fgsea

                   Changes in version 1.21.1                        

FindIT2

             Changes in version 1.0.3 (2021-12-29)                  

fishpond

                    Changes in version 2.2.0                        

flowAI

                   Changes in version 1.25.3                        

flowSpecs

             Changes in version 1.9.2 (2022-02-15)                  

fmrs

                    Changes in version 2.0.0                        

IMPROVEMENTS SINCE LAST RELEASE

BUG FIXES

fobitools

                    Changes in version 1.3.2                        

FRASER

                    Changes in version 1.6.1                        

gdsfmt

                   Changes in version 1.32.0                        

UTILITIES

GeneNetworkBuilder

                   Changes in version 1.37.2                        

GENESIS

                   Changes in version 2.25.5                        

GeneTonic

                    Changes in version 2.0.0                        

New features

Other notes

GenomeInfoDb

                   Changes in version 1.32.0                        

DEPRECATED AND DEFUNCT

GenomicAlignments

                   Changes in version 1.32.0                        

GenomicDataCommons

                   Changes in version 1.20.0                        

New features

Bug fixes and minor improvements

GenomicFeatures

                   Changes in version 1.48.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

GenomicRanges

                   Changes in version 1.48.0                        

NEW FEATURES

DEPRECATED AND DEFUNCT

BUG FIXES

GenomicScores

                    Changes in version 2.8.0                        

USER VISIBLE CHANGES

BUG FIXES

GenomicSuperSignature

                    Changes in version 1.4.0                        

GenProSeq

             Changes in version 0.99.0 (2021-09-20)                 

GeoDiff

                    Changes in version 1.1.2                        

GeomxTools

                   Changes in version 2.99.2                        

New features:

New features:

Bug fixes:

New features:

GEOquery

                   Changes in version 2.63.2                        

ggmanh

                   Changes in version 0.99.0                        

ggmsa

                    Changes in version 1.1.4                        

updated the way smooth is invoked on simplot(2022-01-03, Mon)

added smoothed curve on simplot.(2021-12-17, Fri)

                    Changes in version 1.1.3                        

fixed the typo in “posHighligthed”, and changed it to snake_case “position_highlight” from camelCase “posHighligthed” (2021-12-13, Mon)

                    Changes in version 1.1.2                        

fixed the assignment error on line 155 ‘seqlogo.R’

                    Changes in version 1.1.1                        
fixed error: using   instead of on 110 lines in geom_msa.R

ggtree

                    Changes in version 3.3.3                        

ggtreeExtra

                    Changes in version 1.5.4                        

GOSemSim

                   Changes in version 2.21.1                        

graphite

             Changes in version 1.41.2 (2022-04-21)                 

GSVA

                    Changes in version 1.50                         

BUG FIXES

Harman

                   Changes in version 1.23.1                        

HDF5Array

                   Changes in version 1.24.0                        

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

hermes

                   Changes in version 0.99.4                        

Miscellaneous

New Features

Bug Fixes

Miscellaneous

New Features

HIBAG

                   Changes in version 1.32.0                        

HiCDCPlus

             Changes in version 1.3.1 (2022-01-23)                  

hpar

                    Changes in version 1.37                         

Changes in version 1.37.1

HPAStainR

             Changes in version 1.4.1 (2021-11-23)                  

HPiP

             Changes in version 1.1.1 (2021-11-29)                  

HubPub

             Changes in version 1.3.0 (2021-11-24)                  

idr2d

                    Changes in version 1.8.1                        

IgGeneUsage

             Changes in version 1.9.3 (2022-03-31)                  

illuminaio

             Changes in version 3.24.0 (2021-05-19)                 

imcRtools

             Changes in version 1.1.9 (2022-04-19)                  

immunoClust

                   Changes in version 1.27.6                        

infercnv

             Changes in version 1.11.2 (2022-02-03)                 

InPAS

                    Changes in version 2.3.1                        

InteractiveComplexHeatmap

                    Changes in version 1.3.1                        

InterCellar

             Changes in version 2.2.0 (2022-04-06)                  

IntEREst

                   Changes in version 1.20.0                        

NEW FEATURES

IRanges

                   Changes in version 2.30.0                        

SIGNIFICANT USER-VISIBLE CHANGES

ISAnalytics

             Changes in version 1.5.4 (2022-04-20)                  

MAJOR CHANGES

NEW FEATURES

MINOR CHANGES

BUG FIXES

DEPRECATED FUNCTIONS

MINOR CHANGES

NEW (MINOR)

MINOR CHANGES

FIXES

FIXES

iSEEu

                    Changes in version 1.7.1                        

IsoformSwitchAnalyzeR

            Changes in version 1.17.04 (2022-01-06)                 

karyoploteR

                    Changes in version 1.21.0

BUG FIXES

kebabs

                   Changes in version 1.29.1                        

LACE

                     Changes in version 2.0                         

limma

                   Changes in version 3.52.0                        

lineagespot

             Changes in version 0.99.0 (2021-09-21)                 

LinTInd

                   Changes in version 0.99.1                        

Bugfixes

First built

NEWS.md setup

maftools

                   Changes in version 2.12.00                       

(GitHub master branch/BC 3.15 RC)

NEW FUNCTIONS

ENHANCEMENTS

MAGeCKFlute

                   Changes in version 1.99.0                        

MassSpecWavelet

             Changes in version 1.61.3 (2022-04-05)                 

MatrixQCvis

             Changes in version 1.3.8 (2022-04-12)                  

MBECS

                   Changes in version 0.99.13                       

mbOmic

                    Changes in version 0.99.3

UPDATE MAIN CLASSES

ADD NEW FUNCTIONS

memes

                    Changes in version 1.2.5                        

meshr

                    Changes in version 2.0.2                        

metabCombiner

                    Changes in version 1.5.2                        

MetaboAnnotation

                    Changes in version 0.99                         

Changes in 0.99.15

Changes in 0.99.14

Changes in 0.99.13

Changes in 0.99.12

Changes in 0.99.11

Changes in 0.99.10

Changes in 0.99.9

Changes in 0.99.8

Changes in 0.99.7

Changes in 0.99.5

Changes in 0.99.4

Changes in 0.99.3

Changes in 0.2.11

Changes in 0.2.10

Changes in 0.2.9

Changes in 0.2.8

Changes in 0.2.7

Changes in 0.2.6

Changes in 0.2.5

Changes in 0.2.4

Changes in 0.2.3

Changes in 0.2.2

Changes in 0.2.1

Changes in 0.2.0

MetaboCoreUtils

                     Changes in version 1.3                         

MetaboCoreUtils 1.3.8

MetaboCoreUtils 1.3.7

MetaboCoreUtils 1.3.6

MetaboCoreUtils 1.3.5

MetaboCoreUtils 1.3.4

MetaboCoreUtils 1.3.3

MetaboCoreUtils 1.3.2

MetaboCoreUtils 1.3.1

MetNet

             Changes in version 1.13.2 (2022-03-04)                 

mia

                     Changes in version 1.3                         

miaViz

                     Changes in version 1.3                         

microbiome

             Changes in version 1.17.2 (2022-02-15)                 

microbiomeMarker

                    Changes in version 1.1.2                        

MicrobiotaProcess

                   Changes in version 1.7.11                        

miloR

             Changes in version 1.3.1 (2022-01-07)                  

mirTarRnaSeq

             Changes in version 1.3.2 (2022-04-06)                  

mistyR

                    Changes in version 1.4.0                        

MLP

                   Changes in version 1.43.1                        

MobilityTransformR

                    Changes in version 0.99                         

monaLisa

                    Changes in version 1.1.2                        

Motif2Site

                   Changes in version 0.99.5                        

motifStack

                   Changes in version 1.39.4                        

MouseFM

             Changes in version 1.4.2 (2022-02-28)                  

MQmetrics

                    Changes in version 1.3.3                        

msa

                   Changes in version 1.27.2                        

MSA2dist

             Changes in version 0.99.3 (2022-03-18)                 

Major changes

Minor improvements and bug fixes

Major changes

Minor improvements and bug fixes

Major changes

Minor improvements and bug fixes

Major changes

Minor improvements and bug fixes

MsBackendMassbank

                     Changes in version 1.3                         

Changes in 1.3.5

Changes in 1.3.4

Changes in 1.3.3

Changes in 1.3.2

Changes in 1.3.1

MsBackendMgf

                     Changes in version 1.3                         

Changes in 1.3.3

Changes in 1.3.2

Changes in 1.3.1

MsBackendMsp

                    Changes in version 0.99                         

Changes in 0.99.4

Changes in 0.99.2

Changes in 0.99.1

Changes in 0.98.2

Changes in 0.98.1

Changes in 0.98.0

MsBackendRawFileReader

                     Changes in version 1.1                         

MsCoreUtils

                     Changes in version 1.7                         

MsCoreUtils 1.7.5

MsCoreUtils 1.7.4

MsCoreUtils 1.7.3

MsCoreUtils 1.7.2

MsCoreUtils 1.7.1

MsCoreUtils 1.7.0

MSnbase

                    Changes in version 2.21                         

Changes in 2.21.7

Changes in 2.21.6

Changes in 2.21.5

Changes in 2.21.4

Changes in 2.21.3

Changes in 2.21.2

Changes in 2.21.1

msPurity

                   Changes in version 1.21.2                        

MSstatsConvert

                    Changes in version 1.5.1                        

MSstatsTMT

             Changes in version 2.2.7 (2022-02-18)                  

MuData

                   Changes in version 0.99.0                        

MultiAssayExperiment

                   Changes in version 1.22.0                        

Bug fixes and minor improvements

multiHiCcompare

             Changes in version 1.13.0 (2022-04-21)                 

MungeSumstats

                   Changes in version 1.3.18                        

New features

New features

Bug fixes

New features

Bug fixes

New Features

Bug fixes

New Features

Bug fixes

New Features

Bug fixes

Bug fixes

New Features

Bug fixes

Bug fixes

New Features

Bug fixes

New Features

Bug fixes

New Features

muscat

                    Changes in version 1.9.3                        

mzR

                   Changes in version 2.29.4                        

NanoMethViz

                    Changes in version 2.2.0                        

NanoStringNCTools

             Changes in version 1.3.1 (2022-01-12)                  

ndexr

                   Changes in version 1.17.0                        

nnSVG

             Changes in version 0.99.0 (2022-03-02)                 

NormalyzerDE

                   Changes in version 1.13.2                        

nullranges

                    Changes in version 1.1.4                        

NxtIRFcore

             Changes in version 1.1.1 (2022-01-11)                  

OGRE

                   Changes in version 0.99.8                        

orthogene

                    Changes in version 1.1.5                        

BUG FIXES

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

BUG FIXES

NEW FEATURES

BUG FIXES

NEW FEATURES

PanomiR

                   Changes in version 0.99.0                        

pareg

            Changes in version 0.99.22 (2022-02-18)                 

pcaExplorer

                   Changes in version 2.22.0                        

Other notes

Bug fixes

peakPantheR

             Changes in version 1.9.2 (2022-04-18)                  

pengls

                    Changes in version 1.1.2                        

phantasus

                   Changes in version 1.15.7                        

PhIPData

             Changes in version 1.3.3 (2022-02-04)                  

PhosR

                    Changes in version 1.5.1                        

PhyloProfile

                    Changes in version 1.8.6                        

Pigengene

            Changes in version 1.21.40 (2022-04-15)                 

Changes in existing functions

Changes in existing functions

Changes in existing functions

New functions

plotgardener

                   Changes in version 1.1.18                        

NEW FEATURES

NEW FEATURES

BUG FIXES

BUG FIXES

BUG FIXES

BUG FIXES

BUG FIXES

NEW FEATURES

polyester

                   Changes in version 1.99.3                        

POMA

                   Changes in version 1.5.16                        

preciseTAD

             Changes in version 1.5.0 (2022-04-21)                  

progeny

           Changes in version 2020-10-14 (2020-10-14)               

Major update with the following main points:

pRolocGUI

                     Changes in version 2.5                         

CHANGES IN VERSION 2.5.4

CHANGES IN VERSION 2.5.3

CHANGES IN VERSION 2.5.2

CHANGES IN VERSION 2.5.1

CHANGES IN VERSION 2.5.0

ProteoDisco

                    Changes in version 1.1.3                        

protGear

            Changes in version 0.99.546 (2022-03-25)                

ProtGenerics

                   Changes in version 1.27.1                        

psichomics

                   Changes in version 1.20.2                        

PSMatch

                    Changes in version 0.99                         

Changes in 0.99.5

Changes in 0.99.4

Changes in 0.99.3

Changes in 0.99.2

Changes in 0.99.1

Changes in 0.99.0

PureCN

                    Changes in version 2.2.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUGFIXES

QDNAseq

             Changes in version 1.31.0 (2021-10-27)                 

RELEASE

QFeatures

                     Changes in version 1.5                         

QFeatures 1.5.2

QFeatures 1.5.1

QFeatures 1.5.0

qmtools

             Changes in version 0.99.3 (2022-04-12)                 

qpgraph

                    Changes in version 2.30                         

BUG FIXES

qPLEXanalyzer

                   Changes in version 1.13.2                        

qsea

                   Changes in version 1.21.2                        

qsvaR

                   Changes in version 0.99.0                        

NEW FEATURES

Qtlizer

             Changes in version 1.8.1 (2022-02-28)                  

RAREsim

              Changes in version 0.99.4

rawrr

              Changes in version 1.3 (2022-03-19)                   

Rbwa

                    Changes in version 1.0.0                        

RcisTarget

                    Changes in version 1.15                         

RCM

                   Changes in version 1.11.3                        

Rcpi

             Changes in version 1.31.1 (2022-04-25)                 

Improvements

RCy3

                   Changes in version 2.16.0                        

ReactomeGSA

             Changes in version 1.9.1 (2021-11-05)                  

recountmethylation

                    Changes in version 1.5.1                        

RedeR

                    Changes in version 2.0.0                        

rgoslin

                    Changes in version 0.99                         

Please note that this Bioconductor version is based on Goslin version 2.0.0. See the Goslin repository for more details.

Changes in 0.99.1

rgsepd

                    Changes in version 1.27                         

rhdf5

                   Changes in version 2.40.0                        

NEW FEATURES

CHANGES

BUG FIXES

Rhdf5lib

                    Changes in version 1.18                         

New features

Rhtslib

                   Changes in version 1.28.0                        

SIGNIFICANT USER-VISIBLE CHANGES

RiboDiPA

                    Changes in version 1.3.1                        

ribosomeProfilingQC

                    Changes in version 1.7.1                        

RMassBank

                    Changes in version 3.5.1                        

RnaSeqSampleSize

             Changes in version 2.5.1 (2021-12-02)                  

NEW FEATURES

BUG FIXES

RnBeads

                   Changes in version 2.13.2                        

RolDE

                   Changes in version 0.99.4                        

rols

                    Changes in version 2.23                         

CHANGES IN VERSION 2.23.2

CHANGES IN VERSION 2.23.1

CHANGES IN VERSION 2.23.0

ropls

                   Changes in version 1.27.8                        

MINOR MODIFICATION

MINOR MODIFICATION

MINOR MODIFICATION

MINOR MODIFICATION

rpx

                    Changes in version 2.3.0                        

rpx 2.3.3

rpx 2.3.2

rpx 2.3.1

rpx 2.3.0

rrvgo

                    Changes in version 1.7.1                        

Rsubread

                   Changes in version 2.10.0                        

rWikiPathways

                   Changes in version 1.16.0                        

S4Vectors

                   Changes in version 0.34.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

satuRn

                    Changes in version 1.3.1                        

SCArray

                    Changes in version 1.4.0                        

scater

                   Changes in version 1.24.0                        

scDblFinder

             Changes in version 1.9.11 (2022-04-16)                 

scPCA

             Changes in version 1.9.1 (2022-01-19)                  

scTensor

                    Changes in version 2.4.1                        

sechm

             Changes in version 1.3.1 (2022-04-15)                  

seqArchR

                  Changes in version 0.99.339                       

New features

Breaking changes

SeqArray

                   Changes in version 1.36.0                        

NEW FEATURES

UTILITIES

BUG FIXES

seqcombo

                   Changes in version 1.17.1                        

SEtools

             Changes in version 1.9.2 (2022-04-16)                  

signatureSearch

             Changes in version 1.9.6 (2022-01-28)                  

simplifyEnrichment

                    Changes in version 1.5.2                        

singleCellTK

                    Changes in version 2.5.2                        

sitePath

                   Changes in version 1.11.2                        

SNPRelate

                   Changes in version 1.30.0                        

sparrow

                     Changes in version 1.2                         

Enhancements

Bug Fixes

SpatialDecon

             Changes in version 1.5.0 (2021-10-27)                  

SpatialExperiment

             Changes in version 1.5.3 (2022-02-28)                  

spatialHeatmap

             Changes in version 2.1.1 (2022-04-06)                  

spatzie

                    Changes in version 1.0.1                        

Spectra

                     Changes in version 1.5                         

Changes in 1.5.20

Changes in 1.5.19

Changes in 1.5.18

Changes in 1.5.17

Changes in 1.5.16

Changes in 1.5.15

Changes in 1.5.14

Changes in 1.5.13

Changes in 1.5.12

Changes in 1.5.11

Changes in 1.5.10

Changes in 1.5.9

Changes in 1.5.8

Changes in 1.5.7

Changes in 1.5.6

Changes in 1.5.5

Changes in 1.5.4

Changes in 1.5.3

Changes in 1.5.2

Changes in 1.5.1

SpectralTAD

             Changes in version 1.11.0 (2022-04-21)                 

splatter

             Changes in version 1.20.0 (2022-04-27)                 

• Better initialisation of fitting as suggested by the InferCNV package

• Additional fallback method

SplicingFactory

                    Changes in version 1.3.1                        

SPOTlight

                   Changes in version 0.99.1                        

sSNAPPY

                   Changes in version 0.99.1

standR

                   Changes in version 0.99.0                        

statTarget

                   Changes in version 1.25.4                        

STdeconvolve

                    Changes in version 0.99.10

struct

                    Changes in version 1.7.1                        

structToolbox

                    Changes in version 1.7.2                        

SummarizedExperiment

                   Changes in version 1.26.0                        

DEPRECATED AND DEFUNCT

SynExtend

                   Changes in version 1.7.14                        

systemPipeShiny

                   Changes in version 1.5.10                        

Major Change

Minor Change

TADCompare

             Changes in version 1.5.0 (2022-04-21)                  

TargetSearch

                   Changes in version 1.52.0                        

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

BUG FIXES

TBSignatureProfiler

                    Changes in version 1.7.1                        

Bug Fixes

Major Changes

Minor Changes

TCGAutils

                   Changes in version 1.16.0                        

New features

Minor changes and bug fixes

TFEA.ChIP

                   Changes in version 1.15.2                        

New ChIP-Gene databases available

New Features

New default database

tomoda

                    Changes in version 1.5.0                        

tomoseqr

             Changes in version 0.99.0 (2022-03-28)                 

topdownr

                    Changes in version 1.17                         

Changes in version 1.17.3

Changes in version 1.17.2

Changes in version 1.17.1

trackViewer

                   Changes in version 1.31.4                        

transformGamPoi

                     Changes in version 1.1                         

transite

                   Changes in version 1.12.1                        

treeio

                   Changes in version 1.19.2                        

TREG

                   Changes in version 0.99.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

tricycle

                    Changes in version 1.3.4                        

tximeta

                   Changes in version 1.14.0                        

UCell

                    Changes in version 2.0.0                        

universalmotif

                   Changes in version 1.14.0                        

NEW FEATURES

MINOR CHANGES

BUG FIXES

BUG FIXES

BUG FIXES

BUG FIXES

updateObject

                    Changes in version 1.0.0                        

variancePartition

                   Changes in version 1.25.13                       

VaSP

             Changes in version 1.7.2 (2022-01-07)                  

velociraptor

                    Changes in version 1.5.2                        

vissE

                    Changes in version 1.4.0                        

weitrix

                    Changes in version 1.7.1                        

xcms

                   Changes in version 3.17.6                        

zellkonverter

                    Changes in version 1.6.0                        

Major changes

Minor changes

NEWS from new and existing Data Experiment Packages

crisprScoreData

                   Changes in version 0.99.0                        

curatedMetagenomicData

                    Changes in version 3.4.0                        

depmap

                     Changes in version 1.9                         

Changes in version 1.9.2

Changes in version 1.9.1

Changes in version 1.9.0

Changes in version 1.7.1

Changes in version 1.7.0

dorothea

             Changes in version 1.7.1 (2022-04-07)                  

epimutacionsData

                   Changes in version 0.99.7                        

FlowSorted.Blood.EPIC

             Changes in version 1.99.1 (2022-01-04)                 

healthyControlsPresenceChecker

            Changes in version 0.99.17 (2021-11-29)                 

msdata

                   Changes in version 0.35.3                        

pRolocdata

                   Changes in version 1.33.1                        

scpdata

                     Changes in version 1.3                         

scpdata 1.3.1

scpdata 1.3.0

signatureSearchData

             Changes in version 1.9.3 (2021-12-16)                  

spatialLIBD

                   Changes in version 1.7.19                        

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

NEW FEATURES

NEW FEATURES

BUG FIXES

NEW FEATURES

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

NEW FEATURES

STexampleData

             Changes in version 1.3.3 (2022-01-31)                  

tuberculosis

                    Changes in version 1.2.0                        

NEWS from new and existing Workflows

GeoMxWorkflows

                    Changes in version 1.1.2                        

Deprecated and Defunct Packages

Twenty one software packages were removed from this release (after being deprecated in Bioc 3.14): affyPara, ALPS, alsace, BrainStars, dualKS, ENCODExplorer, ENVISIONQuery, FindMyFriends, GeneAnswers, gramm4R, KEGGprofile, MSGFgui, MSGFplus, MSstatsTMTPTM, PanVizGenerator, predictionet, RGalaxy, scClassifR, slinky, SRGnet, SwimR

Please note: destiny and MouseFM, previously announced as deprecated in 3.14, fixed their packages and remained in Bioconductor.

Twenty nine software packages are deprecated in this release and will be removed in Bioc 3.16: ABAEnrichment, Autotuner, CAnD, caOmicsV, CHETAH, clonotypeR, CountClust, diffloop, GCSConnection, GCSFilesystem, GenoGAM, genphen, gprege, networkBMA, Onassis, perturbatr, phemd, ppiStats, ProteomicsAnnotationHubData, PSICQUIC, PubScore, Rgin, RmiR, RpsiXML, ScISI, SLGI, Sushi, tofsims, TSRchitect

Three experimental data packages were removed from this release (after being deprecated in BioC 3.14): ABAData, brainImageRdata, tcgaWGBSData.hg19

Please note: PCHiCdata and RITANdata previously announced as deprecated in 3.14, fixed their packages and remained in Bioconductor.

Three experimental data packages are deprecated in this release and will be removed in Bioc 3.16: DREAM4, MSstatsBioData, ppiData

One annotation packages was removed from this release (after being deprecated in Bioc 3.14): org.Pf.plasmo.db

One annotation package was deprecated in this release and will be removed in Bioc 3.16: MafH5.gnomAD.v3.1.1.GRCh38_3.13.1.tar.gz

No workflow packages were removed from this release (after being deprecated in Bioc 3.14)

One workflow package was deprecated in this release and will be removed in 3.16: proteomics