April 26, 2023

Bioconductors:

We are pleased to announce Bioconductor 3.17, consisting of 2230 software packages, 419 experiment data packages, 912 annotation packages, 27 workflows and 3 books.

There are 79 new software packages, 7 new data experiment packages, no new annotation packages, 2 new workflows, no new books, and many updates and improvements to existing packages.

Bioconductor 3.17 is compatible with R 4.3, and is supported on Linux, 64-bit Windows, Intel 64-bit macOS 11 (Big Sur) or higher and macOS arm64. 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 3.17

To update to or install Bioconductor 3.17:

  1. Install R 4.3. Bioconductor 3.17 has been designed expressly for this version of R.

  2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 79 new software packages in this release of Bioconductor.

New Data Experiment Packages

There are 7 new data experiment packages in this release of Bioconductor.

New Annotation Packages

There are no new annotation packages.

New Workflow Packages

There are 2 new workflow packages in this release of Bioconductor.

New Online Books

There are no new online books.

NEWS from existing Software Packages

ADaCGH2

             Changes in version 2.39.1 (2023-04-14)                 

affxparser

             Changes in version 1.73.0 (2023-04-25)                 

Notes

Notes

Bug Fixes

Bug Fixes

Notes

AHMassBank

                    Changes in version 0.99                         

AHMassBank 0.99.3

AHMassBanki 0.99.0

alevinQC

                   Changes in version 1.15.1                        

AlpsNMR

             Changes in version 4.1.6 (2023-02-16)                  

AneuFinder

                   Changes in version 1.27.1                        

SIGNIFICANT USER-LEVEL CHANGES

AnnotationForge

                   Changes in version 1.41.0                        

MODIFICATIONS

ENHANCEMENT

AnnotationHub

                    Changes in version 3.7.0                        

NEW FEATURES

DEPRECATED

AnnotationHubData

                   Changes in version 1.29.0                        

NEW FEATURES

AnVIL

                   Changes in version 1.12.0                        

USER VISIBLE CHANGES

BUG FIXES

AnVILWorkflow

                    Changes in version 1.0.0                        

aroma.light

             Changes in version 3.31.0 (2023-04-25)                 

Notes

Notes

ArrayExpress

                   Changes in version 1.58.0                        

ATACseqQC

                   Changes in version 1.23.1                        

ATACseqTFEA

                    Changes in version 1.1.1                        

atena

             Changes in version 1.6.0 (2023-04-20)                  

USER VISIBLE CHANGES

BUG FIXES

BASiCS

             Changes in version 2.11.9 (2023-03-07)                 

basilisk.utils

                   Changes in version 1.12.0                        

batchelor

                   Changes in version 1.16.0                        

benchdamic

             Changes in version 1.5.3 (2023-04-20)                  

BiocCheck

                   Changes in version 1.36.0                        

NEW FEATURES

BUG FIXES AND MINOR IMPROVEMENTS

BiocFileCache

                     Changes in version 2.7                         

USER VISIBLE CHANGE

BUG FIX

BiocHail

                    Changes in version 1.0.0                        

BiocHubsShiny

                    Changes in version 1.0.0                        

BiocIO

                   Changes in version 1.10.0                        

Significant user-visible changes

BiocParallel

                    Changes in version 1.34                         

NEW FEATURES

USER VISIBLE CHANGES

BUG FIXES

BiocPkgTools

                   Changes in version 1.18.0                        

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

BiocSet

                    Changes in version 1.14                         

BUG FIX

BiocStyle

                   Changes in version 2.28.0                        

BUG FIXES

biocthis

                    Changes in version 1.9.2                        

BUG FIXES

biocViews

                   Changes in version 1.67.0                        

ENHANCEMENT

biodbHmdb

             Changes in version 1.5.1 (2023-03-22)                  

biomaRt

                   Changes in version 2.56.0                        

BUG FIXES

BioNAR

                    Changes in version 1.2.1                        

bluster

                   Changes in version 1.10.0                        

BRGenomics

                   Changes in version 1.11.1                        

BridgeDbR

                    Changes in version 2.9.2                        

NEW FEATURES

NEW FEATURES

BSgenomeForge

                    Changes in version 1.0.0                        

CAGEr

                    Changes in version 2.6.0                        

BUG FIXES

NEW FEATURES

Cardinal

             Changes in version 3.0.1 (2022-11-14)                  

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

cBioPortalData

                   Changes in version 2.12.0                        

Bug fixes and minor improvements

CBNplot

             Changes in version 0.99.5 (2023-04-13)                 

celda

             Changes in version 1.14.2 (2023-01-19)                 

cellxgenedp

                     Changes in version 1.4                         

SIGNIFICANT USER-VISIBLE CHANGES

CeTF

                   Changes in version 1.11.1                        

cfDNAPro

                    Changes in version 1.5.4                        

cfTools

                    Changes in version 1.0.0                        

ChIPpeakAnno

                   Changes in version 3.33.1                        

ChIPQC

                   Changes in version 1.35.1                        

ChIPseeker

                   Changes in version 1.35.3                        

ClassifyR

                    Changes in version 3.4.0                        

clevRvis

             Changes in version 0.99.5 (2023-01-16)                 

clusterProfiler

                    Changes in version 4.7.1                        

CNVfilteR

                   Changes in version 1.13.2                        

MINOR

MINOR

cogeqc

                    Changes in version 1.3.1                        

CHANGES

cola

                    Changes in version 2.5.4                        

compcodeR

                   Changes in version 1.35.1                        

ComplexHeatmap

                   Changes in version 2.15.3                        

CompoundDb

                     Changes in version 1.3                         

Changes in version 1.3.3

Changes in version 1.3.2

Changes in version 1.3.2

Changes in version 1.3.0

concordexR

                   Changes in version 0.99.0                        

CoSIA

                   Changes in version 0.99.0                        

COTAN

                   Changes in version 1.99.3                        

Updated the vignette, README.md and NEWS.md

                   Changes in version 1.99.2                        

Dropped second vignette: will be merged in the other one…

                   Changes in version 1.99.1                        

Minor bug fixes and new function clustersMarkersHeatmapPlot()

                   Changes in version 1.99.0                        

Included new functionalities for Bioc 2.17 release:

crisprBase

                    Changes in version 1.3.3                        

crisprBowtie

                    Changes in version 1.3.2                        

crisprDesign

                   Changes in version 1.1.25                        

crisprScore

                    Changes in version 1.3.4                        

csdR

                    Changes in version 1.5.1                        

CTdata

                    Changes in version 0.99                         

CTdata 0.99.0

cytofQC

             Changes in version 0.99.3 (2022-11-11)                 

cytomapper

             Changes in version 1.11.3 (2023-01-23)                 

CytoML

                    Changes in version 3.11                         

API Changes

Fixes/internal changes

API Changes

Fixes/internal changes

CytoPipeline

                    Changes in version 0.99                         

CytoPipeline 0.99.6

CytoPipeline 0.99.5

CytoPipeline 0.99.4

CytoPipeline 0.99.3

CytoPipeline 0.99.2

CytoPipeline 0.99.1

CytoPipeline 0.99.0

cytoviewer

             Changes in version 0.99.3 (2023-04-18)                 

dearseq

             Changes in version 1.11.1 (2023-03-16)                 

deconvR

                    Changes in version 1.5.2                        

deepSNV

             Changes in version 1.99.3 (2013-07-25)                 

Updates

Bugfixes

Updates

Bugfixes

Updates

Bugfixes

Updates

DelayedArray

                   Changes in version 0.26.0                        

DELocal

                   Changes in version 0.99.1                        

DepInfeR

             Changes in version 1.3.1 (2023-04-04)                  

DESeq2

                   Changes in version 1.39.8                        

DESpace

                    Changes in version 1.0.0                        

DiffBind

                    Changes in version 3.9.4                        

DNAfusion

                    Changes in version 1.3.0                        

doubletrouble

                   Changes in version 0.99.3                        

BUG FIXES

CHANGES

NEW FEATURES

edgeR

                   Changes in version 3.42.0                        

enrichplot

                   Changes in version 1.19.2                        

ensembldb

                   Changes in version 2.23.2                        

EpiCompare

                    Changes in version 1.3.4                        

New features

Bug fixes

New features

Bug fixes

New features

Bug fixes

EpiDISH

                   Changes in version 2.15.0                        

epigraHMM

                    Changes in version 1.7.2                        

epistack

             Changes in version 1.5.4 (2022-04-05)                  

erccdashboard

                   Changes in version 1.33.1                        

SIGNIFICANT USER-VISIBLE CHANGES / BUG FIX

escheR

                   Changes in version 0.99.8                        

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

EWCE

                    Changes in version 1.7.3                        

New features

Bug fixes

New features

Bug fixes

New features

ExperimentHub

                    Changes in version 2.7.1                        

DEPRECATE

extraChIPs

                    Changes in version 1.3.9                        

FeatSeekR

                   Changes in version 0.99.1                        

fgsea

                   Changes in version 1.25.1                        

fishpond

                    Changes in version 2.5.4                        

flowGate

             Changes in version 0.99.3 (2023-03-15)                 

FlowSOM

                    Changes in version 2.7.9                        

flowSpecs

             Changes in version 1.13.1 (2023-04-05)                 

fmrs

                    Changes in version 2.0.0                        

IMPROVEMENTS SINCE LAST RELEASE

BUG FIXES

gdsfmt

                   Changes in version 1.36.0                        

UTILITIES

NEW FEATURES

UTILITIES

genbankr

                   Changes in version 1.27.1                        

BUGFIXES

GeneTonic

                    Changes in version 2.4.0                        

New features

Other notes

GenomAutomorphism

                    Changes in version 1.0.3                        

GenomeInfoDb

                   Changes in version 1.36.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

GenomicAlignments

                   Changes in version 1.36.0                        

NEW FEATURES

BUG FIXES

GenomicDataCommons

                   Changes in version 1.24.0                        

Bug fixes and minor improvements

GenomicFeatures

                   Changes in version 1.52.0                        

NEW FEATURES

DEPRECATED AND DEFUNCT

BUG FIXES

GenomicRanges

                   Changes in version 1.52.0                        

SIGNIFICANT USER-VISIBLE CHANGES

GeoTcgaData

                   Changes in version 0.99.2                        

ggtree

                    Changes in version 3.7.2                        

ggtreeDendro

                    Changes in version 1.1.3                        

ggtreeExtra

                    Changes in version 1.9.2                        

glmGamPoi

              Changes in version 1.11 (2023-01-03)                  

GRaNIE

             Changes in version 1.3.34 (2023-03-29)                 

Bugfixes

New features and vignette updates

  1. getGRNSummary() that summarizes a GRN object and returns a named list, which can be used to compare different GRN objects ore easily among each other, for example.
  2. plotCorrelations() for scatter plots of the underlying data for either TF-peak, peak-gene or TF-gene pairs. This can be useful to visualize specific TF-peak, peak-gene or TF-gene pairs to investigate the underlying data and to judge the reasonability of the inferred connection.

Bugfixes

New features and vignette updates

Bugfixes

New features and vignette updates

Improvements

Bugfixes

New features and vignette updates

Minor changes

Bug fixes

Minor changes

Bug fixes

New features

New features

Bug fixes

New features

Bug fixes

Minor changes

Bug fixes

Minor changes

Major changes

Bug fixes

Bug fixes

Minor changes

New features

New features

Minor changes

Major changes

Minor changes

New features

graphite

             Changes in version 1.45.1 (2023-04-19)                 

hca

                     Changes in version 1.8                         

New features

HDF5Array

                   Changes in version 1.28.0                        

HIBAG

                   Changes in version 1.34.1                        

HiCDOC

             Changes in version 1.1.1 (2022-11-30)                  

HilbertCurve

                   Changes in version 1.29.1                        

hipathia

             Changes in version 2.99.0 (2022-12-01)                 

HPAanalyze

                    Changes in version 1.17                         

hpar

                    Changes in version 1.41                         

Changes in version 1.41.1

IFAA

                   Changes in version 0.99.8                        

illuminaio

             Changes in version 0.43.0 (2023-04-25)                 

Notes

Notes

imcRtools

             Changes in version 1.5.5 (2023-04-20)                  

immunoClust

                   Changes in version 1.31.12                       

infercnv

             Changes in version 1.15.3 (2023-03-29)                 

INTACT

                   Changes in version 0.99.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

InteractiveComplexHeatmap

                    Changes in version 1.7.1                        

IntEREst

                   Changes in version 1.24.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

IRanges

                   Changes in version 2.34.0                        

SIGNIFICANT USER-VISIBLE CHANGES

ISAnalytics

             Changes in version 1.9.3 (2023-04-04)                  

ENHANCES AND REFACTORING

FIXES AND GENERAL UPDATES

DEPRECATIONS & BREAKING CHANGES

MINOR CHANGES

FIXES AND GENERAL UPDATES

iSEE

                   Changes in version 2.11.4                        

iSEEhub

                    Changes in version 1.1.1                        

MINOR UPDATES

iSEEu

                   Changes in version 1.11.2                        

IsoformSwitchAnalyzeR

                   Changes in version 2.01.14                       

kebabs

                   Changes in version 1.33.2                        

limma

                   Changes in version 3.56.0                        

magpie

                   Changes in version 0.99.10                       

mariner

                   Changes in version 0.99.0                        

Bug fixes and improvements:

Methods for pulling Hi-C pixels and matrices from .hic files and storing them on-disk with HDF5Array and DelayedArray.

Overview of functionality

New or updated functions:

First pre-release of mariner functionality focused on manipulating, clustering, and merging paired interactions.

Overview of functionality

MassSpecWavelet

             Changes in version 1.65.1 (2023-04-07)                 

mastR

                   Changes in version 0.99.9                        

MatrixQCvis

             Changes in version 1.7.7 (2023-04-20)                  

matter

                    Changes in version 2.1.1                        

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

MBECS

                    Changes in version 1.3.1                        

mbQTL

             Changes in version 0.99.6 (2023-03-30)                 

MEB

                   Changes in version 1.13.1                        

metabCombiner

                    Changes in version 1.9.2                        

metabinR

             Changes in version 1.2.0 (2023-04-21)                  

MetaboAnnotation

                     Changes in version 1.3                         

Changes in 1.3.2

Changes in 1.3.1

MetCirc

             Changes in version 1.29.2 (2023-04-18)                 

MetNet

             Changes in version 1.17.1 (2022-11-23)                 

mia

                     Changes in version 1.7                         

miaViz

             Changes in version 1.7.2 (2022-02-17)                  

MicrobiotaProcess

                   Changes in version 1.11.5                        

microSTASIS

             Changes in version 0.99.0 (2022-09-25)                 

miQC

             Changes in version 1.7.1 (2023-01-04)                  

mirTarRnaSeq

             Changes in version 1.7.1 (2023-04-12)                  

mistyR

                     Changes in version 1.7                         

                    Changes in version 1.6.1                        

MoleculeExperiment

             Changes in version 0.99.5 (2023-04-17)                 

msa

                   Changes in version 1.31.7                        

MSA2dist

             Changes in version 1.3.1 (2022-11-08)                  

Major changes

Minor improvements and bug fixes

MsBackendMassbank

                     Changes in version 1.7                         

Changes in 1.7.4

Changes in 1.7.3

Changes in 1.7.2

Changes in 1.7.1

MsBackendMgf

                     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

Changes in 1.7.0

MsBackendMsp

                     Changes in version 1.3                         

Changes in 1.3.1

MsBackendSql

                    Changes in version 0.99                         

Changes in 0.99.7

Changes in 0.99.6

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

Changes in 0.98.1

Changes in 0.98.0

Changes in 0.1.0

MsCoreUtils

                    Changes in version 1.11                         

MsCoreUtils 1.11.6

MsCoreUtils 1.11.5

MsCoreUtils 1.11.4

MsCoreUtils 1.11.3

MsCoreUtils 1.11.2

MsCoreUtils 1.11.1

MsCoreUtils 1.11.0

MsDataHub

                    Changes in version 0.99                         

MsDataHub 0.99.3

MsDataHub 0.99.2

MsDataHub 0.99.1

MsDataHub 0.99.0

MsExperiment

                     Changes in version 1.1                         

MsExperiment 1.1.4

MsExperiment 1.1.3

MsExperiment 1.1.2

MsExperiment 1.1.1

MsExperiment 1.1.0

MSnbase

                    Changes in version 2.25                         

MSnbase 2.25.2

MSnbase 2.25.1

MSnbase 2.25.0

MsQuality

                    Changes in version 0.99                         

Changes in version 0.99.9 (2023-04-18)

Changes in version 0.99.8 (2023-09-02)

Changes in version 0.99.7 (2023-06-02)

Changes in version 0.99.6 (2022-11-29):

Changes in version 0.99.5 (2022-10-12):

Changes in version 0.99.4 (2022-10-11):

Changes in version 0.99.3 (2022-10-11):

Changes in version 0.99.2 (2022-09-20):

Changes in version 0.99.1 (2021-11-23)

Changes in version 0.99.0 (2021-09-10)

MSstatsConvert

                    Changes in version 1.9.1                        

MSstatsTMT

             Changes in version 2.6.1 (2023-02-26)                  

MultiAssayExperiment

                   Changes in version 1.26.0                        

New features

Bug fixes and minor improvements

MultimodalExperiment

                   Changes in version 0.99.0                        

MungeSumstats

                   Changes in version 1.7.18                        

New features

New features

Bug fix

Bug fix

New features

Bug fix

New features

New features

Bug fix

Bug fix

Bug fix

New features

New features

muscat

                   Changes in version 1.12.1                        

mzR

                   Changes in version 2.33.1                        

NanoMethViz

                    Changes in version 2.6.0                        

NanoStringNCTools

             Changes in version 1.7.1 (2022-01-25)                  

NanoTube

                    Changes in version 1.5.1                        

ndexr

                   Changes in version 1.21.1                        

netZooR

                    Changes in version 1.3.2                        

ngsReports

                    Changes in version 2.1.5                        

nullranges

                   Changes in version 1.5.19                        

oncoscanR

                    Changes in version 1.1.0                        

OncoSimulR

             Changes in version 4.1.4 (2023-03-08)                  

OrganismDbi

                   Changes in version 1.41.1                        

MODIFICATIONS

orthogene

                    Changes in version 1.5.2                        

New features

Bug fixes

New features

Bug fixes

OUTRIDER

                   Changes in version 1.16.1                        

OutSplice

             Changes in version 0.99.9 (2023-04-17)                 

pairedGSEA

                   Changes in version 0.99.6                        

peakPantheR

            Changes in version 1.13.21 (2023-03-28)                 

pfamAnalyzeR

             Changes in version 0.99.7 (2023-04-18)                 

phantasus

                   Changes in version 1.19.3                        

PharmacoGx

                    Changes in version 3.3.2                        

phenomis

                    Changes in version 1.1.2                        

PhosR

                    Changes in version 1.9.1                        

PhyloProfile

                   Changes in version 1.14.0                        

Pigengene

            Changes in version 1.25.16 (2023-03-22)                 

Changes in existing functions

Changes in existing functions

Changes in existing functions

Changes in existing functions

planttfhunter

                   Changes in version 0.99.2                        

CHANGES

NEW FEATURES

plotgardener

                    Changes in version 1.5.3                        

BUG FIXES

BUG FIXES

BUG FIXES

Version bump for Bioconductor 3.16 release.

PoDCall

             Changes in version 1.7.1 (2023-04-04)                  

podkat

                   Changes in version 1.31.1                        

polyester

                   Changes in version 1.99.3                        

pRoloc

                    Changes in version 1.39                         

Changes in version 1.39.1

Changes in version 1.39.0

pRolocGUI

                    Changes in version 2.9.0                        

CHANGES IN VERSION 2.9.0

CHANGES IN VERSION 2.9.1

protGear

             Changes in version 1.3.32 (2022-12-11)                 

PSMatch

                     Changes in version 1.3                         

PSMatch 1.3.3

PSMatch 1.3.2

PSMatch 1.3.1

QFeatures

                     Changes in version 1.9                         

QFeatures 1.9.4

QFeatures 1.9.3

QFeatures 1.9.2

QFeatures 1.9.1

QFeatures 1.9.0

qsea

                   Changes in version 1.25.1                        

qsmooth

             Changes in version 1.15.1 (2022-11-04)                 

QuasR

                   Changes in version 1.40.0                        

USER-VISIBLE CHANGES

RaggedExperiment

                   Changes in version 1.24.0                        

Bug fixes and minor improvements

Rarr

                   Changes in version 0.99.9                        

rawrr

             Changes in version 1.7.12 (2023-03-17)                 

Rbwa

                    Changes in version 1.3.1                        

Rcollectl

Initial Submission

RCy3

                   Changes in version 2.20.0                        

ReactomeGSA

             Changes in version 1.13.1 (2023-04-13)                 

RESOLVE

                    Changes in version 1.2.0                        

retrofit

             Changes in version 0.99.0 (2023-03-05)                 

ReUseData

                   Changes in version 0.99.23                       

rgoslin

                    Changes in version 1.4.0                        

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

BioConductor 3.17 - Changes in 1.4.0

Improvements

Bug Fixes

BioConductor 3.16 - Changes in 1.2.0

BioConductor 3.15 - Changes in 1.0.0

Improvements

Bug Fixes

Changes in 0.99.1

rGREAT

                    Changes in version 2.1.9                        

rhdf5

                   Changes in version 2.44.0                        

CHANGES

BUG FIXES

rhdf5filters

                   Changes in version 1.12.0                        

USER VISIBLE CHANGES

BUG FIXES

Rhdf5lib

                    Changes in version 1.22                         

User visible changes

Rhtslib

                    Changes in version 2.2.0                        

ribosomeProfilingQC

                   Changes in version 1.11.1                        

rifiComparative

                   Changes in version 0.99.5                        

RnBeads

                   Changes in version 2.17.1                        

ROTS

                   Changes in version 1.27.1                        

rpx

                     Changes in version 2.7                         

rpx 2.7.4

rpx 2.7.3

rpx 2.7.2

rpx 2.7.1

rrvgo

                   Changes in version 1.10.1                        

Rsamtools

                    Changes in version 2.16                         

NEW FEATURES

RTCGAToolbox

                   Changes in version 2.30.0                        

New features

Bug fixes and minor improvements

S4Arrays

                    Changes in version 1.0.0                        

S4Vectors

                   Changes in version 0.38.0                        

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

SAIGEgds

                    Changes in version 2.0.0                        

NEW FEATURES

sangeranalyseR

                    Changes in version 99.1                         

scAnnotatR

             Changes in version 1.5.3 (2023-03-19)                  

SCArray

                    Changes in version 1.8.0                        

SCArray.sat

                   Changes in version 0.99.0                        

scater

                   Changes in version 1.28.0                        

scBubbletree

                    Changes in version 1.1.8                        

scDblFinder

            Changes in version 1.13.10 (2023-03-23)                 

scp

                     Changes in version 1.9                         

scp 1.9.2

scp 1.9.1

scp 1.9.0

scran

                    Changes in version 1.28                         

scReClassify

                    Changes in version 1.5.1                        

screenCounter

                    Changes in version 1.2.0                        

scRNAseqApp

                    Changes in version 1.1.1                        

scuttle

                    Changes in version 1.10                         

seq.hotSPOT

                   Changes in version 0.99.6                        

seqArchRplus

                  Changes in version 0.99.0.10                      

New

New

New

Bug-fixes

New features

Bux-fixes

New features

New

SeqArray

                   Changes in version 1.40.0                        

SGCP

             Changes in version 0.99.0 (2022-10-06)                 

ShortRead

                    Changes in version 1.58                         

BUG FIXES

signeR

                    Changes in version 2.1.1                        

signifinder

                    Changes in version 1.1.1                        

SimBu

             Changes in version 1.1.2 (2023-01-12)                  

simplifyEnrichment

                    Changes in version 1.9.1                        

singleCellTK

             Changes in version 2.8.1 (2022-03-10)                  

SiPSiC

                   Changes in version 0.99.2                        

SNPRelate

                   Changes in version 1.34.0                        

SparseArray

                    Changes in version 1.0.0                        

spaSim

                    Changes in version 1.1.2                        

BUG FIXES

SIGIFICANT USER CHANGE

SpatialExperiment

             Changes in version 1.9.5 (2023-03-02)                  

SpatialFeatureExperiment

                    Changes in version 1.1.6                        

spatialHeatmap

             Changes in version 2.5.4 (2023-04-14)                  

SpatialOmicsOverlay

             Changes in version 0.99.0 (2022-04-01)                 

speckle

                   Changes in version 0.99.7                        

Spectra

                     Changes in version 1.9                         

Changes in 1.9.15

Changes in 1.9.14

Changes in 1.9.13

Changes in 1.9.12

Changes in 1.9.11

Changes in 1.9.10

Changes in 1.9.9

Changes in 1.9.8

Changes in 1.9.7

Changes in 1.9.6

Changes in 1.9.5

Changes in 1.9.4

Changes in 1.9.3

Changes in 1.9.2

Changes in 1.9.1

Changes in 1.9.0

SpectralTAD

             Changes in version 1.15.3 (2023-03-07)                 

SPIAT

                    Changes in version 1.1.6                        

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

NOTES

BUG FIXES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Development version on Bioconductor 3.17.

splatter

             Changes in version 1.24.0 (2022-04-26)                 

SpliceWiz

             Changes in version 1.1.8 (2023-04-17)                  

SpotClean

                    Changes in version 1.1.2                        

standR

                    Changes in version 1.3.9                        

statTarget

                     Changes in version 2.0                         

NEW FEATURES

stJoincount

                    Changes in version 1.1.1                        

SummarizedExperiment

                   Changes in version 1.30.0                        

DEPRECATED AND DEFUNCT

surfaltr

             Changes in version 1.5.1 (2022-08-12)                  

SVMDO

            Changes in version 0.99.24 (2023-04-22)                 

synapsis

           Changes in version 2021-07-02 (2021-07-02)               

Changes:

SynExtend

                   Changes in version 1.11.8                        

synlet

                   Changes in version 1.99.0                        

NEW FEATURES

syntenet

                    Changes in version 1.1.6                        

BUG FIXES

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

UPDATES

BUG FIXES

NEW FEATURES

NEW FEATURES

systemPipeShiny

                   Changes in version 1.9.04                        

Major Change

Minor Change

Bug Fix

TargetSearch

                    Changes in version 2.2.0                        

BUG FIXES

TBSignatureProfiler

                   Changes in version 1.92.0                        

Bug Fixes

Major Changes

Minor Changes

TCGAutils

                   Changes in version 1.20.0                        

New features

TDbasedUFE

                   Changes in version 0.99.7                        

TDbasedUFEadv

            Changes in version 0.99.21 (2023-04-14)                 

TENxIO

                    Changes in version 1.2.0                        

New features

Bug fixes and minor improvements

terraTCGAdata

                    Changes in version 1.4.0                        

New features

tomoseqr

             Changes in version 1.11.1 (2022-10-25)                 

TPP

                   Changes in version 3.27.1                        

trackViewer

                   Changes in version 1.35.5                        

treeio

                   Changes in version 1.23.1                        

tRNA

             Changes in version 1.17.1 (2022-12-19)                 

tximeta

                   Changes in version 1.17.2                        

tximport

                   Changes in version 1.27.1                        

UniProt.ws

                   Changes in version 2.40.0                        

USER VISIBLE CHANGES

BUG FIXES AND MINOR IMPROVEMENTS

universalmotif

                   Changes in version 1.18.0                        

NEW FEATURES

MINOR CHANGES

BUG FIXES

updateObject

                    Changes in version 1.4.0                        

variancePartition

                   Changes in version 1.28.9                        

velociraptor

                    Changes in version 1.9.2                        

Voyager

                   Changes in version 1.1.12                        

weitrix

                   Changes in version 1.11.1                        

xcms

                   Changes in version 3.21.5                        

zellkonverter

                   Changes in version 1.10.0                        

Major changes

Minor changes

zenith

                    Changes in version 1.1.2                        

ZygosityPredictor

             Changes in version 0.99.0 (2023-02-22)                 

NEWS from existing Data Experiment Packages

CoSIAdata

New Package Release

curatedTCGAData

                   Changes in version 1.22.0                        

Bug fixes and minor improvements

gDNAinRNAseqData

                    Changes in version 1.0.0                        

USER VISIBLE CHANGES

imcdatasets

             Changes in version 1.7.3 (2023-02-26)                  

marinerData

                   Changes in version 0.99.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

MetaScope

                   Changes in version 0.99.0                        

microRNAome

                   Changes in version 1.21.1                        

pRolocdata

                   Changes in version 1.37.1                        

scMultiome

                   Changes in version 0.99.5                        

NEWS.md setup

SFEData

                    Changes in version 1.2.0                        

SingleCellMultiModal

                   Changes in version 1.12.0                        

Bug fixes and minor improvements

spatialLIBD

                   Changes in version 1.11.13                       

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

NEWS from existing Workflows

seqpac

Deprecated and Defunct Packages

Thirty two software packages were removed from this release (after being deprecated in Bioc 3.16): 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

Please note: coMET, previously announced as deprecated in 3.16, has been updated and remain in Bioconductor.

Thirty five software packages are deprecated in this release and will be removed in Bioc 3.18: alpine, ArrayExpressHTS, ASpediaFI, BiocDockerManager, ChIC, chromswitch, copynumber, CopywriteR, dasper, epihet, GAPGOM, gcatest, GeneAccord, genotypeeval, lfa, maanova, metavizr, MethCP, MIGSA, MIMOSA, NanoStringQCPro, NBSplice, netboxr, NxtIRFcore, ODER, pkgDepTools, PrecisionTrialDrawer, proBatch, proFIA, pulsedSilac, savR, sigPathway, STAN, TarSeqQC, tscR

Two experimental data packages were removed from this release (after being deprecated in BioC 3.16): gatingMLData, RNASeqRData

Two experimental data packages are deprecated in this release and will be removed in Bioc 3.18: alpineData, plasFIA

No annotation packages were removed from this release (after being deprecated in Bioc 3.16).

No annotation packages were deprecated in this release and will be removed in Bioc 3.18.

No workflow package was removed from this release (after being deprecated in Bioc 3.16).

No workflow packages were deprecated in this release and will be removed in 3.18.