November 2, 2022

Bioconductors:

We are pleased to announce Bioconductor 3.16, consisting of 2183 software packages, 416 experiment data packages, 909 annotation packages, 28 workflows and 8 books.

There are 71 new software packages, 9 new data experiment packages, 1 new annotation packages, no new workflows, no new books, and many updates and improvements to existing packages.

Bioconductor 3.16 is compatible with R 4.2, and is supported on Linux, 64-bit Windows, and Intel 64-bit macOS 10.13 (High Sierra) or higher. Bioconductor is excited to start supporting arm64 with this release. This release will also 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 3.16

To update to or install Bioconductor 3.16:

  1. Install R 4.2. Bioconductor 3.16 has been designed expressly for this version of R.

  2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 71 new software packages in this release of Bioconductor.

New Data Experiment Packages

There are 9 new data experiment packages in this release of Bioconductor.

New Annotation Packages

There are 2 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 existing Software Packages

affxparser

             Changes in version 1.69.1 (2022-04-28)                 

BUG FIXES

BUG FIXES

alevinQC

                   Changes in version 1.13.2                        

AlpsNMR

             Changes in version 4.1.1 (2022-11-02)                  

Minor changes

Minor changes

Minor changes

Major changes

Minor changes

Breaking changes

Major changes

Minor changes

ANCOMBC

              Changes in version 2.0 (2022-10-19)                   

AnnotationForge

                   Changes in version 1.39.0                        

MODIFICATIONS

AnnotationHub

                    Changes in version 3.5.0                        

NEW FEATURES

AnVIL

                   Changes in version 1.10.0                        

NEW FEATURES

USER VISIBLE CHANGES

Rawls

$removed [1] admin_delete_refresh_token admin_statistics_get 3 refreshToken refreshTokenDate

$updated [1] listUserBillingAccounts createWorkspace getTags [4] clone entity_type_metadata get_entity [7] entityQuery createSubmission validateSubmission

Terra

$removed [1] userTrial listImportPFBJobs importPFBStatus

$updated [1] deleteBillingProject billingAccounts 3 createWorkspace cloneWorkspace [5] entityQuery flexibleImportEntities [7] importEntities createSubmission [9] validateSubmission browserDownloadEntitiesTSV [11] setProfile

Leonardo

$removed [1] batchNodepoolCreate

$updated [1] listApp listAppByProject deleteApp [4] createApp listDisks listDisksByProject [7] createDisk updateRuntime createRuntime [10] setCookie proxyClusterJupyter proxyClusterJupyterLab [13] proxyClusterRStudio

BUG FIXES

AnVILPublish

                    Changes in version 1.8.0                        

New Features

User Visible Changes

Bug Fixes

aroma.light

             Changes in version 3.27.0 (2022-04-26)                 

ATACCoGAPS

             Changes in version 0.99.0 (2022-03-04)                 

ATACseqQC

                   Changes in version 1.21.2                        

AUCell

                    Changes in version 1.19                         

bandle

                     Changes in version 1.1                         

bandle 1.1.3

bandle 1.1.2

bandle 1.1.1

version 1.1.0

BASiCS

             Changes in version 2.9.7 (2022-09-06)                  

BASiCStan

                     Changes in version 1.0                         

beachmat

                   Changes in version 2.14.0                        

BEclear

             Changes in version 2.13.2 (2022-09-21)                 

beer

             Changes in version 1.1.3 (2022-06-26)                  

benchdamic

             Changes in version 1.3.11 (2022-10-31)                 

BindingSiteFinder

                     Changes in version 1.4                         

BiocBaseUtils

                    Changes in version 1.0.0                        

BiocCheck

                    Changes in version 1.34                         

NEW FEATURES

BUG FIXES AND MINOR IMPROVEMENTS

BiocFHIR

                    Changes in version 1.0.0                        

BiocFileCache

                     Changes in version 2.5                         

ENHANCEMENT

BUG FIX

BiocParallel

                    Changes in version 1.32                         

NEW FEATURES

USER VISIBLE CHANGES

BUG FIXES

BiocPkgTools

                   Changes in version 1.16.0                        

SIGNIFICANT USER-VISIBLE CHANGES

biocthis

                    Changes in version 1.7.0                        

NEW FEATURES

BUG FIXES

biocViews

                   Changes in version 1.65.0                        

ENHANCEMENT

BioNAR

                  Changes in version 0.99.001                       

biosigner

                   Changes in version 1.25.6                        

MINOR MODIFICATION

MINOR MODIFICATION

NEW FEATURE

BridgeDbR

                    Changes in version 2.7.5                        

BUG FIXES

NEW FEATURES

NEW FEATURES

BUG FIXES

cageminer

                    Changes in version 1.3.3                        

NEW FEATURES

Cardinal

             Changes in version 2.99.1 (2022-10-31)                 

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

cbaf

             Changes in version 1.20.0 (2022-10-24)                 

New Features

cBioPortalData

                   Changes in version 2.10.0                        

New features

Bug fixes and minor improvements

celda

             Changes in version 1.13.0 (2022-10-20)                 

CellBarcode

                    Changes in version 1.2.2                        

Enhancements

New features

Bug fix

cellxgenedp

                     Changes in version 1.2                         

SIGNIFICANT USER-VISIBLE CHANGES

OTHER

ChIPanalyser

                   Changes in version 1.19.0                        

Package Updates

ChIPpeakAnno

                   Changes in version 3.31.4                        

ChIPQC

                   Changes in version 1.33.1                        

ChIPseeker

                   Changes in version 1.33.4                        

CHRONOS

                   Changes in version 1.25.1                        

CircSeqAlignTk

             Changes in version 0.99.0 (2022-08-09)                 

ClassifyR

                    Changes in version 3.2.0                        

cleaver

             Changes in version 1.35.1 (2022-08-31)                 

clusterExperiment

                   Changes in version 2.17.3                        

clusterProfiler

                    Changes in version 4.5.3                        

CNVfilteR

                   Changes in version 1.11.1                        

BUG FIXES

cogeqc

                    Changes in version 1.1.8                        

CHANGES

BUG FIXES

BUG FIXES

NEW FEATURES

NEW FEATURES

NEW FEATURES

coMET

             Changes in version 1.29.2 (2022-10-26)                 

compEpiTools

                   Changes in version 1.31.1                        

ComplexHeatmap

                   Changes in version 2.13.4                        

CompoundDb

                     Changes in version 1.1                         

Changes in version 1.1.6

Changes in version 1.1.5

Changes in version 1.1.4

Changes in version 1.1.3

Changes in version 1.1.2

Changes in version 1.1.1

CoreGx

                    Changes in version 2.1.7                        

cTRAP

                   Changes in version 1.14.1                        

cytomapper

             Changes in version 1.9.2 (2022-10-24)                  

CytoML

                    Changes in version 3.11                         

API Changes

Fixes/internal changes

API Changes

Fixes/internal changes

                   Changes in version 1.35.1                        

dcanr

             Changes in version 1.14.0 (2022-10-11)                 

dearseq

             Changes in version 1.9.4 (2022-07-20)                  

decompTumor2Sig

             Changes in version 2.13.1 (2022-05-09)                 

deepSNV

             Changes in version 1.99.3 (2013-07-25)                 

Updates

Bugfixes

Updates

Bugfixes

Updates

Bugfixes

Updates

Bugfixes

DegNorm

                    Changes in version 1.7.1                        

DEGreport

                   Changes in version 1.33.2                        

DelayedArray

                   Changes in version 0.24.0                        

SIGNIFICANT USER-VISIBLE CHANGES

DExMA

                    Changes in version 1.5.1                        

DiffBind

                     Changes in version 3.8                         

DifferentialRegulation

                    Changes in version 1.0.7                        

Dino

                    Changes in version 1.3.1                        

dittoSeq

                    Changes in version 1.10                         

DOSE

                   Changes in version 3.23.3                        

DropletUtils

                   Changes in version 1.18.0                        

edgeR

                   Changes in version 3.40.0                        

enrichplot

                   Changes in version 1.17.4                        

ensembldb

                   Changes in version 2.21.5                        

EpiCompare

                    Changes in version 1.1.2                        

New features

Bug fixes

New features

Bug fixes

epimutacions

                    Changes in version 1.1.2                        

EWCE

                    Changes in version 1.5.8                        

Bug fixes

Bug fixes

Bug fixes

New features

Bug fixes

New features

New features

Bug fixes

New features

Bug fixes

exomePeak2

             Changes in version 1.8.1 (2022-05-16)                  

ExploreModelMatrix

                    Changes in version 1.9.2                        

extraChIPs

             Changes in version 1.1.5 (2022-10-11)                  

fastreeR

             Changes in version 1.3.0 (2022-11-01)                  

fgga

             Changes in version 1.5.0 (2022-07-13)                  

fgsea

                   Changes in version 1.23.1                        

FindIT2

                    Changes in version 1.2.3                        

fishpond

                    Changes in version 2.4.0                        

FlowSOM

                    Changes in version 2.5.6                        

flowSpecs

              Changes in version 1.11 (2022-07-23)                  

fmrs

                    Changes in version 2.0.0                        

IMPROVEMENTS SINCE LAST RELEASE

BUG FIXES

FRASER

                    Changes in version 1.8.1                        

gage

                   Changes in version 2.47.1                        

gdsfmt

                   Changes in version 1.34.0                        

UTILITIES

GeneNetworkBuilder

                   Changes in version 1.39.2                        

GeneTonic

                    Changes in version 2.2.0                        

New features

Other notes

GenomeInfoDb

                   Changes in version 1.34.0                        

NEW FEATURES

DEPRECATED AND DEFUNCT

GenomicAlignments

                   Changes in version 1.34.0                        

BUG FIXES

GenomicFeatures

                   Changes in version 1.50.0                        

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

GenomicFiles

                    Changes in version 1.34                         

BUG FIXES

GenomicRanges

                   Changes in version 1.50.0                        

GenomicScores

                   Changes in version 2.10.0                        

USER VISIBLE CHANGES

BUG FIXES

GeomxTools

                    Changes in version 3.1.1                        

ggmsa

                    Changes in version 1.3.3                        

ggspavis

             Changes in version 1.3.1 (2022-10-11)                  

ggtree

                    Changes in version 3.6.0                        

ggtreeExtra

                    Changes in version 1.7.1                        

glmGamPoi

                     Changes in version 1.9                         

GOSemSim

                   Changes in version 2.23.1                        

GRaNIE

             Changes in version 1.1.21 (2022-12-13)                 

Major changes

Minor changes

Major changes

Minor changes

Minor changes

Bug fixes

graphite

             Changes in version 1.43.2 (2022-10-31)                 

GreyListChIP

                   Changes in version 1.29.1                        

GSVA

                    Changes in version 1.46                         

BUG FIXES

HDF5Array

                   Changes in version 1.26.0                        

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

hermes

                    Changes in version 1.0.1                        

Herper

                    Changes in version 1.6.1                        

HIBAG

                   Changes in version 1.34.0                        

HiCDCPlus

             Changes in version 1.5.2 (2022-06-06)                  

hipathia

             Changes in version 2.13.1 (2022-07-27)                 

HPAanalyze

                    Changes in version 1.15                         

IgGeneUsage

         Changes in version 1.11.2-1.11.11 (2022-10-24)             

illuminaio

             Changes in version 0.41.0 (2022-11-01)                 

Miscellaneous

Bug Fixes

imcRtools

             Changes in version 1.3.10 (2022-10-22)                 

immunoClust

                   Changes in version 1.29.2                        

infercnv

             Changes in version 1.13.1 (2022-10-17)                 

InteractiveComplexHeatmap

                    Changes in version 1.5.1                        

IRanges

                   Changes in version 2.32.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

ISAnalytics

             Changes in version 1.7.6 (2022-10-25)                  

VISIBLE USER CHANGES

BUG FIXES AND MINOR CHANGES

BUG FIXES AND MINOR CHANGES

NEW

BUG FIXES AND MINOR CHANGES

NEW

BUG FIXES AND MINOR CHANGES

iSEE

                   Changes in version 2.9.12                        

iSEEu

                    Changes in version 1.9.3                        

isomiRs

                   Changes in version 1.25.1                        

FIX

kebabs

                   Changes in version 1.31.2                        

KEGGREST

                   Changes in version 1.37.0                        

BUG CORRECTION

limma

                   Changes in version 3.54.0                        

goana() and kegga() now call goanaTrend() when the trend argument is used. When plot=TRUE the plot is now created by goanaTrend() instead of by barcodeplot().

MassSpecWavelet

             Changes in version 1.63.6 (2022-10-15)                 

MatrixGenerics

                    Changes in version 1.9.1                        

MatrixQCvis

             Changes in version 1.5.9 (2022-10-19)                  

matter

             Changes in version 1.99.2 (2022-10-31)                 

BUG FIXES

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

memes

                    Changes in version 1.5.2                        

metabCombiner

                    Changes in version 1.7.1                        

MetaboAnnotation

                     Changes in version 1.1                         

Changes in 1.1.6

Changes in 1.1.5

Changes in 1.1.4

Changes in 1.1.3

Changes in 1.1.2

Changes in 1.1.1

MetaboCoreUtils

                     Changes in version 1.5                         

MetaboCoreUtils 1.5.2

MetaboCoreUtils 1.5.1

MetCirc

             Changes in version 1.27.2 (2022-10-19)                 

MetNet

             Changes in version 1.15.2 (2022-05-18)                 

mia

                     Changes in version 1.5                         

miaViz

                     Changes in version 1.5                         

microbiomeExplorer

                    Changes in version 1.7.1                        

microbiomeMarker

                    Changes in version 1.3.2                        

MicrobiotaProcess

                    Changes in version 1.9.5                        

midasHLA

                    Changes in version 1.5.2                        

minfi

                    Changes in version 1.43                         

miRspongeR

                 Changes in version 2.1.1-2.1.3                     

mirTarRnaSeq

             Changes in version 1.5.1 (2022-07-21)                  

mistyR

                     Changes in version 1.5                         

Modstrings

             Changes in version 1.13.1 (2022-08-13)                 

monaLisa

                    Changes in version 1.3.1                        

motifStack

                   Changes in version 1.41.1                        

msa

                   Changes in version 1.29.3                        

MSA2dist

             Changes in version 1.1.7 (2022-10-05)                  

Major changes

Minor improvements and bug fixes

             Changes in version 1.1.6 (2022-09-22)                  

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

Major changes

Minor improvements and bug fixes

Major changes

Minor improvements and bug fixes

MsBackendMgf

                     Changes in version 1.5                         

Changes in 1.5.1

MsCoreUtils

                     Changes in version 1.9                         

MsCoreUtils 1.9.2

MsCoreUtils 1.9.1

MsCoreUtils 1.9.0

msImpute

                    Changes in version 1.7.1                        

mslp

                   Changes in version 0.99.6                        

NEW FEATURES

FIXES

MSnbase

                    Changes in version 2.23                         

Changes in 2.23.2

Changes in 2.23.1

Changes in 2.23.0

msqrob2

                    Changes in version 1.5.3                        

MSstatsTMT

             Changes in version 2.4.1 (2022-09-12)                  

MultiAssayExperiment

                   Changes in version 1.24.0                        

New features

Bug fixes and minor improvements

MungeSumstats

                   Changes in version 1.5.18                        

Bug fix

New features

New features

Bug fix

Bug fixes

New features

Bug fixes

Bug fixes

Bug fixes

Bug fixes

New features

Bug fixes

Bug fixes

New features

Bug fixes

New features

Bug fixes

New features

Bug fixes

New features

Bug fixes

muscat

                   Changes in version 1.11.1                        

NanoMethViz

                    Changes in version 2.4.0                        

NanoTube

                    Changes in version 1.3.7                        

ndexr

                   Changes in version 1.19.1                        

netZooR

                   Changes in version 1.1.12                        

ngsReports

                    Changes in version 2.0.0                        

nnSVG

             Changes in version 1.1.2 (2022-05-17)                  

NxtIRFcore

             Changes in version 1.3.2 (2022-10-25)                  

oncoscanR

                    Changes in version 1.1.0                        

OncoSimulR

                     Changes in version 4.0                         

orthogene

                    Changes in version 1.3.4                        

Bug fixes

Bug fixes

New features

Bug fixes

New features

New features

Bug fixes

pathview

                   Changes in version 1.37.1                        

peakPantheR

             Changes in version 1.11.1 (2022-08-05)                 

pengls

                    Changes in version 1.3.2                        

phantasus

                   Changes in version 1.17.5                        

PharmacoGx

                    Changes in version 3.1.4                        

3.1.0

PhyloProfile

                   Changes in version 1.10.3                        

plotgardener

                    Changes in version 1.3.9                        

BUG FIXES

BUG FIXES

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

Version bump for Bioconductor 3.15 release.

polyester

                   Changes in version 1.99.3                        

POMA

                   Changes in version 1.7.19                        

proDA

                    Changes in version 1.11                         

pRoloc

                    Changes in version 1.37                         

Changes in version 1.37.1

pRolocGUI

                     Changes in version 2.7                         

CHANGES IN VERSION 2.7.2

CHANGES IN VERSION 2.7.1

CHANGES IN VERSION 2.7.0

psichomics

                   Changes in version 1.24.0                        

QDNAseq

             Changes in version 1.33.1 (2022-04-27)                 

MISCELLANEOUS

BUG FIXES

QFeatures

                     Changes in version 1.7                         

QFeatures 1.7.3

QFeatures 1.7.2

QFeatures 1.7.1

QFeatures 1.7.0

qPLEXanalyzer

                   Changes in version 1.15.3                        

quantiseqr

                    Changes in version 1.6.0                        

Other notes

RaggedExperiment

                   Changes in version 1.22.0                        

rawrr

              Changes in version 1.5 (2022-08-22)                   

Rcpi

             Changes in version 1.33.2 (2022-07-17)                 

Improvements

Improvements

Improvements

RCy3

                   Changes in version 2.18.0                        

ReactomePA

                   Changes in version 1.41.1                        

reconsi

                    Changes in version 1.9.1                        

rGREAT

                   Changes in version 1.99.7                        

rhdf5

                   Changes in version 2.42.0                        

CHANGES

BUG FIXES

Rhdf5lib

                    Changes in version 1.20                         

Bug fixes

Rhisat2

                   Changes in version 1.13.1                        

Rhtslib

                    Changes in version 2.0.0                        

SIGNIFICANT USER-VISIBLE CHANGES

RLSeq

                    Changes in version 1.3.0                        

Bioc 3.16 release with the addition of a noise analysis function.

RMassBank

                    Changes in version 3.7.1                        

rmelting

                   Changes in version 1.13.3                        

RnBeads

                   Changes in version 2.15.1                        

rols

                    Changes in version 2.25                         

CHANGES IN VERSION 2.25.5

CHANGES IN VERSION 2.25.4

CHANGES IN VERSION 2.25.3

CHANGES IN VERSION 2.25.2

CHANGES IN VERSION 2.25.1

CHANGES IN VERSION 2.25.0

ropls

                   Changes in version 1.29.32                       

MINOR MODIFICATION

MINOR MODIFICATION

NEW FEATURE

MINOR MODIFICATION

MINOR MODIFICATION

NEW FEATURE

NEW FEATURE

NEW FEATURE

MINOR MODIFICATION

rpx

                     Changes in version 2.5                         

rpx 2.5.1

rpx 2.5.0

rrvgo

                    Changes in version 1.8.1                        

Rsubread

                   Changes in version 2.12.0                        

RTCGA

                   Changes in version 1.27.2                        

RTCGAToolbox

                   Changes in version 2.28.0                        

New features

Bug fixes and minor improvements

S4Vectors

                   Changes in version 0.36.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

sangeranalyseR

                    Changes in version 99.1                         

satuRn

                    Changes in version 1.4.1                        

We report a bug in satuRn 1.4.0. (Bioconductor release 3.15). The bug was inadvertently introduced in satuRn 1.3.1 (from the former Bioconductor devel). Note that the bug was not thus present in any of the older Bioconductor releases 3.13 and 3.14 (satuRn 1.0.x, 1.1.x and 1.2.x).

Bug details:

Imagine a gene with three isoforms and two cell types. The goal is to assess DTU between cell types. All isoforms are expressed in all cells of cell type 1. However, none of the isoforms are expressed in any of the cells in cell type 2 (i.e., the gene is not expressed in cell type 2).

satuRn computes the log-odds of picking a certain isoform from the pool of isoforms in each cell type, and then compares these log-odds estimates between the cell types. However, in this example, the log-odds of picking a certain isoform from the pool of isoforms in cell type 2 cannot be computed, as there is no data. Hence, the DTU test statistic should be NA. However, due to erroneous handling of NA estimates, which was inadvertently introduced in satuRn 1.3.1. while aiming to resolve github issue 16, the log-odds in cell type 1 will be compared to zero. Hence, (erroneous) results can be obtained for this contrast, even when there are no data in cell type 2.

Note that in many cases such isoforms may not pass filtering and would not get evaluated altogether. However, when analyzing sprase scRNA-Seq datasets with a lenient filtering criterium, this problem will apply, and will result in mistakes in the inference.

scater

                   Changes in version 1.26.0                        

SCFA

             Changes in version 1.7.1 (2022-07-29)                  

scp

                     Changes in version 1.7                         

scp 1.7.4

scp 1.7.3

scp 1.7.2

scp 1.7.1

scp 1.7.0

scRepertoire

                    Changes in version 1.7.2                        

scTGIF

                   Changes in version 1.11.1                        

scuttle

                    Changes in version 1.8.0                        

seqArchR

                    Changes in version 1.1.1                        

SeqArray

                   Changes in version 1.38.0                        

UTILITIES

NEW FEATURES

BUG FIXES

BUG FIXES

shinyepico

             Changes in version 1.4.2 (2022-05-18)                  

signeR

                    Changes in version 2.0.0                        

simplifyEnrichment

                    Changes in version 1.7.2                        

singleCellTK

             Changes in version 2.7.3 (2022-10-25)                  

SingleR

                    Changes in version 2.0.0                        

SNPRelate

                   Changes in version 1.32.0                        

SpatialDecon

             Changes in version 1.8.0 (2022-08-09)                  

SpatialExperiment

             Changes in version 1.7.2 (2022-10-07)                  

spatialHeatmap

             Changes in version 2.3.1 (2022-10-22)                  

Spectra

                     Changes in version 1.7                         

Changes in 1.7.5

Changes in 1.7.4

Changes in 1.7.3

Changes in 1.7.2

Changes in 1.7.1

splatter

             Changes in version 1.22.0 (2022-10-31)                 

sSNAPPY

             Changes in version 1.1.1 (2022-08-03)                  

statTarget

                     Changes in version 2.0                         

NEW FEATURES

SummarizedExperiment

                   Changes in version 1.28.0                        

SIGNIFICANT USER-VISIBLE CHANGES

synapter

                    Changes in version 2.21                         

Changes in version 2.21.1

SynExtend

                   Changes in version 1.9.20                        

systemPipeShiny

                   Changes in version 1.7.03                        

General:

Minor change:

Bug fix:

TargetDecoy

             Changes in version 1.3.4 (2022-10-21)                  

TargetSearch

                    Changes in version 2.0.0                        

NEW FEATURES

BUG FIXES

TBSignatureProfiler

                   Changes in version 1.92.0                        

Bug Fixes

Major Changes

Minor Changes

tomoseqr

             Changes in version 1.11.1 (2022-10-25)                 

topdownr

                    Changes in version 1.19                         

Changes in version 1.19.2

Changes in version 1.19.1

trackViewer

                   Changes in version 1.33.8                        

transomics2cytoscape

                    Changes in version 1.7.1                        

DATA or DOCUMENT CHANGES

treeio

                   Changes in version 1.21.3                        

tximeta

                   Changes in version 1.15.3                        

tximport

                   Changes in version 1.25.1                        

UCell

                    Changes in version 2.1.2                        

UniProt.ws

                   Changes in version 2.38.0                        

USER VISIBLE CHANGES

Uniquorn

             Changes in version 2.17.3 (2022-10-13)                 

Fixed parsing problem

Fixed parsing problem

Fixed parsing problem

universalmotif

                   Changes in version 1.16.0                        

NEW FEATURES

MINOR CHANGES

BUG FIXES

BUG FIXES

updateObject

                    Changes in version 1.2.0                        

variancePartition

                   Changes in version 1.27.6                        

vissE

                    Changes in version 1.6.0                        

wppi

             Changes in version 1.5.1 (2022-06-07)                  

zellkonverter

                    Changes in version 1.8.0                        

Major changes

Minor changes

NEWS from existing Data Experiment Packages

curatedMetagenomicData

                    Changes in version 3.6.0                        

depmap

                  Changes in version 1.11.2                        

imcdatasets

             Changes in version 1.5.4 (2022-10-21)                  

NxtIRFdata

             Changes in version 1.3.2 (2022-10-25)                  

RforProteomics

                   Changes in version 1.35.1                        

scpdata

                   Changes in version 1.5.5

spatialLIBD

                   Changes in version 1.9.18                        

BUG FIXES

BUG FIXES

NEW FEATURES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

BUG FIXES

BUG FIXES

STexampleData

             Changes in version 1.5.0 (2022-04-27)                  

TargetSearchData

                   Changes in version 1.36.0                        

NEW FEATURES

NEWS from existing Workflows

GeoMxWorkflows

                    Changes in version 1.4.0                        

SingscoreAMLMutations

             Changes in version 1.12.0 (2022-04-05)                 

Deprecated and Defunct Packages

Twenty eight software packages were removed from this release (after being deprecated in Bioc 3.15): ABAEnrichment, Autotuner, BioPlex, CAnD, caOmicsV, clonotypeR, CountClust, diffloop, GCSConnection, GCSFilesystem, GenoGAM, genphen, gprege, networkBMA, Onassis, perturbatr, ppiStats, ProteomicsAnnotationHubData, PSICQUIC, PubScore, Rgin, RmiR, RpsiXML, ScISI, SLGI, Sushi, tofsims, TSRchitect

Please note: phemd and CHETAH, previously announced as deprecated in 3.15, have been updated and remain in Bioconductor.

Thirty software packages are deprecated in this release and will be removed in Bioc 3.17: AffyCompatible, BAC, BitSeq, BrainSABER, bridge, cellTree, coexnet, conclus, ctgGEM, CytoTree, DEComplexDisease, flowCL, flowUtils, gaia, gpart, inveRsion, IsoGeneGUI, iteremoval, MACPET, PoTRA, rama, Rcade, RNASeqR, scAlign, scMAGeCK, sojourner, TCGAbiolinksGUI, TDARACNE, TimeSeriesExperiment, TraRe, tspair, XCIR

Three experimental data packages were removed from this release (after being deprecated in BioC 3.15): DREAM4, MSstatsBioData, ppiData

Two experimental data packages are deprecated in this release and will be removed in Bioc 3.17: gatingMLData, RNASeqRData

One annotation packages was removed from this release (after being deprecated in Bioc 3.15): MafH5.gnomAD.v3.1.1.GRCh38_3.13.1.tar.gz

No annotation packages were deprecated in this release and will be removed in Bioc 3.17.

One workflow package was removed from this release (after being deprecated in Bioc 3.15) proteomics

No workflow packages were deprecated in this release and will be removed in 3.17.