October 27, 2021

Bioconductors:

We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books.

There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow, no new books, and many updates and improvements to existing packages; Bioconductor 3.14 is compatible with R 4.1.1, and is supported on Linux, 32- and 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.

Bioconductor used Microsoft Azure VMs during our 3.14 release process for a critical part of our branching process for software packages. These VMs are available to Bioconductor through our collaboration with the Microsoft Genomics team.

Contents

Getting Started with Bioconductor 3.14

To update to or install Bioconductor 3.14:

  1. Install R 4.1.1. Bioconductor 3.14 has been designed expressly for this version of R.

  2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 89 new software packages in this release of Bioconductor.

New Data Experiment Packages

There are 13 new data experiment packages in this release of Bioconductor.

New Annotation Packages

There are 10 new annotation packages in this release of Bioconductor.

New Workflow Packages

There is 1 new workflow package in this release of Bioconductor.

New Books

There are no new online books.

NEWS from new and existing Software Packages

a4Classif

                   Changes in version 1.41.1                        

affxparser

             Changes in version 1.65.3 (2021-09-22)                 

SOFTWARE QUALITY

SOFTWARE QUALITY

BUG FIXES

AlpsNMR

             Changes in version 3.3.4 (2021-09-16)                  

ANCOMBC

             Changes in version 1.3.2 (2021-08-05)                  

AnnotationHub

                    Changes in version 3.1.0                        

MAJOR UPDATES

USER-VISIBLE MODIFICATIONS

BUG CORRECTION

AnVIL

                    Changes in version 1.6.0                        

NEW FEATURES

USER VISIBLE CHANGES

AnVILPublish

                    Changes in version 1.4.0                        

New Features

APAlyzer

             Changes in version 1.7.3 (2021-08-01)                  

aroma.light

             Changes in version 3.23.1 (2021-08-19)                 

DOCUMENTATION

artMS

             Changes in version 1.10.2 (2021-07-13)                 

ASpli

                    Changes in version 2.3.1                        

BUG FIXES

ATACseqQC

                   Changes in version 1.17.1                        

atena

            Changes in version 0.99.36 (2021-08-01)                 

USER VISIBLE CHANGES

BASiCS

             Changes in version 2.5.7 (2021-10-05)                  

BayesSpace

                    Changes in version 1.3.1                        

Minor improvements and fixes

Minor improvements and fixes

benchdamic

             Changes in version 0.99.4 (2021-10-15)                 

BgeeDB

                   Changes in version 2.18.1                        

BindingSiteFinder

                   Changes in version 0.99.10                       

BiocCheck

                    Changes in version 1.29                         

NEW FEATURES

BUG FIXES

BiocFileCache

                     Changes in version 2.1                         

MAJOR UPDATES

BiocParallel

                    Changes in version 1.28                         

USER VISIBLE CHANGES

BUG FIXES

BiocPkgTools

                   Changes in version 1.12.0                        

NEW FEATURES

BUG FIXES

BiocStyle

                   Changes in version 2.22.0                        

USER-VISIBLE CHANGES

BUG FIXES AND IMPROVEMENTS TO HTML STYLE

biocthis

                    Changes in version 1.3.8                        

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

NEW FEATURES

biocViews

                   Changes in version 1.61.0                        

ENHANCEMENT

biodb

             Changes in version 1.1.16 (2021-10-19)                 

biodbChebi

             Changes in version 0.99.6 (2021-10-12)                 

biodbHmdb

             Changes in version 0.99.4 (2021-10-18)                 

biodbKegg

             Changes in version 0.99.4 (2021-10-13)                 

biodbLipidmaps

             Changes in version 0.99.3 (2021-10-18)                 

biodbUniprot

             Changes in version 0.99.4 (2021-10-12)                 

biomaRt

                   Changes in version 2.50.0                        

MINOR CHANGES

BUG FIXES

BioPlex

                    Changes in version 1.0.0                        

biotmle

                   Changes in version 1.17.0                        

bugsigdbr

                   Changes in version 0.99.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUSseq

            Changes in version 0.99.18 (2020-06-01)                 

cageminer

                   Changes in version 0.99.0                        

NEW FEATURES

CAGEr

                    Changes in version 2.0.0                        

BACKWARDS-INCOMPATIBLE CHANGES

NEW FEATURES

BUG FIXES

Cardinal

                   Changes in version 2.11.3                        

BUG FIXES

BUG FIXES

BUG FIXES

cbaf

             Changes in version 1.16.0 (2021-10-14)                 

New Features

cBioPortalData

                    Changes in version 2.6.0                        

New features

celda

             Changes in version 1.9.3 (2021-10-04)                  

Cepo

                    Changes in version 0.0.1                        

CeTF

                    Changes in version 1.5.4                        

cfDNAPro

                   Changes in version 0.99.1                        

ChIPpeakAnno

                   Changes in version 3.27.7                        

ChIPseeker

                   Changes in version 1.29.2                        

CIMICE

                    Changes in version 1.1.3                        

Overview:

New functionalities:

Overview:

New functionalities:

ClassifyR

                   Changes in version 2.14.0                        

cliProfiler

             Changes in version 0.99.0 (2021-01-22)                 

cliqueMS

                    Changes in version 1.7.0                        

clonotypeR

                   Changes in version 1.32.0                        

DEPRECATION NOTICE

clusterProfiler

                    Changes in version 4.1.4                        

clustifyr

             Changes in version 1.5.2 (2021-10-04)                  

CNVfilteR

                    Changes in version 1.7.4                        

MINOR

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

MINOR

MINOR

cola

                    Changes in version 1.9.1                        

ComplexHeatmap

                    Changes in version 2.9.4                        

conclus

            Changes in version 1.1.002 (2021-08-31)                 

Made the following significant changes

CoreGx

                    Changes in version 1.5.7                        

csdR

                   Changes in version 0.99.6                        

cTRAP

                   Changes in version 1.12.0                        

Web server support (optimised to run in ShinyProxy)

Bug fixes and minor improvements

cytoKernel

                   Changes in version 0.99.0                        

cytomapper

             Changes in version 1.5.4 (2021-09-17)                  

CytoML

                    Changes in version 3.11                         

API Changes

Fixes/internal changes

API Changes

Fixes/internal changes

DaMiRseq

                    Changes in version 2.6.0                        

dasper

                    Changes in version 1.3.2                        

NEW FEATURES

dearseq

             Changes in version 1.5.1 (2021-09-01)                  

decoupleR

                    Changes in version 2.0.0                        

Changes

New features

New features

All new features allow for tidy selection. Making it easier to evaluate different types of data for the same method. For instance, you can specify the columns to use as strings, integer position, symbol or expression.

Methods

Converters

deepSNV

             Changes in version 1.99.3 (2013-07-25)                 

Updates

Bugfixes

Updates

Bugfixes

Updates

Bugfixes

Updates

DegNorm

                    Changes in version 1.3.1                        

DelayedArray

                   Changes in version 0.20.0                        

BUG FIXES

DelayedTensor

                    Changes in version 1.0.0                        

DepecheR

             Changes in version 1.9.1 (2021-10-16)                  

DExMA

                    Changes in version 1.1.2                        

DIAlignR

                    Changes in version 2.1.4                        

DiffBind

                    Changes in version 3.3.4                        

Dino

                   Changes in version 0.99.5                        

distinct

                    Changes in version 1.4.1                        

dittoSeq

                     Changes in version 1.6                         

DOSE

                   Changes in version 3.19.4                        

dStruct

             Changes in version 0.99.3 (2021-05-23)                 

easier

                    Changes in version 0.9.0                        

eisaR

                    Changes in version 1.5.2                        

EnhancedVolcano

                    Changes in version 1.12                         

enrichplot

                   Changes in version 1.13.2                        

ensembldb

                   Changes in version 2.17.4                        

epialleleR

             Changes in version 1.1.9 (2021-09-19)                  

epigraHMM

                    Changes in version 1.0.8                        

escape

                    Changes in version 1.3.1                        

esetVis

                   Changes in version 1.19.1                        

ExperimentHub

                    Changes in version 2.1.0                        

MAJOR UPDATES

FamAgg

                   Changes in version 1.21.2                        

famat

             Changes in version 1.3.1 (2021-10-13)                  

fCCAC

                   Changes in version 1.19.7                        

fgsea

                   Changes in version 1.19.4                        

FindIT2

            Changes in version 0.99.13 (2021-08-11)                 

fishpond

                    Changes in version 2.0.0                        

FLAMES

             Changes in version 0.99.0 (2021-04-15)                 

FlowSOM

                   Changes in version 2.1.24                        

fobitools

                    Changes in version 1.1.9                        

fobitools 1.0.0

gCrisprTools

                    Changes in version 2.0.0                        

MAJOR UPDATE Adding the Following Functionality:

GENESIS

                   Changes in version 2.23.9                        

GeneTonic

                    Changes in version 1.6.0                        

New features

Other notes

GenomeInfoDb

                   Changes in version 1.30.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

GenomicAlignments

                  Changes in version 1.30.0                        

GenomicFeatures

                   Changes in version 1.46.0                        

SIGNIFICANT USER-VISIBLE CHANGES

GenomicRanges

                   Changes in version 1.46.0                        

GenomicSuperSignature

                    Changes in version 1.2.0                        

GeoDiff

                   Changes in version 0.99.5                        

Revisions

Revisions

Revisions

Revisions

Revisions

NEW FEATURES

GeomxTools

ggmsa

                 Changes in version 2021-09-22                      

ggspavis

             Changes in version 0.99.0 (2021-08-08)                 

ggtree

                    Changes in version 3.1.6                        

ggtreeExtra

                    Changes in version 1.3.6                        

glmGamPoi

                     Changes in version 1.5                         

GOfuncR

                   Changes in version 1.13.1                        

USER-LEVEL CHANGES

GOSemSim

                   Changes in version 2.19.1                        

gscreend

                    Changes in version 1.8.0                        

GSEABase

                    Changes in version 1.56                         

SIGNIFICANT USER-VISIBLE CHANGES

GSVA

                    Changes in version 1.50                         

BUG FIXES

HDF5Array

            Changes in version 1.22.0

HDTD

             Changes in version 1.27.1 (2021-07-28)                 

HGC

             Changes in version 1.1.3 (2021-07-06)                  

hiAnnotator

                   Changes in version 1.27.1                        

HIBAG

                   Changes in version 1.30.0                        

HiLDA

             Changes in version 1.7.6 (2020-10-13)                  

hiReadsProcessor

                   Changes in version 1.29.1                        

hpar

                    Changes in version 1.35                         

Changes in version 1.35.1

Changes in version 1.35.0

HPAStainR

                    Changes in version 1.2.1                        

HPiP

            Changes in version 0.99.17 (2021-09-16)                 

hypeR

                    Changes in version 1.9.1                        

ideal

                   Changes in version 1.18.0                        

Bug fixes

Other notes

IgGeneUsage

             Changes in version 1.7.24 (2021-10-14)                 

imcRtools

             Changes in version 0.99.9 (2021-10-22)                 

immunoClust

                   Changes in version 1.25.2                        

immunotation

             Changes in version 1.1.1 (2021-08-09)                  

infercnv

             Changes in version 1.8.1 (2020-08-16)                  

InteractiveComplexHeatmap

                    Changes in version 1.1.4                        

InterCellar

             Changes in version 2.0.0 (2021-10-20)                  

iPath

                    Changes in version 0.99                         

NEW FEATURES

IRanges

                   Changes in version 2.28.0                        

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

ISAnalytics

             Changes in version 1.3.9 (2021-10-25)                  

FIXES

NEW

FIXES

NEW

FIXES

MAJOR CHANGES

NEW

FIXES/MINOR UPDATES

MAJOR CHANGES

MINOR CHANGES

NEW FUNCTIONALITY

FIXES

DEPRECATIONS

OTHER

FIXES

NEW FUNCTIONALITY

MINOR UPDATES

iSEE

                    Changes in version 2.5.3                        

iSEEu

                    Changes in version 1.5.2                        

IsoformSwitchAnalyzeR

            Changes in version 1.15.02 (2021-09-14)                 

isomiRs

                   Changes in version 1.21.1                        

FIX

kebabs

                   Changes in version 1.27.2                        

limma

                   Changes in version 3.50.0                        

LOBSTAHS

                   Changes in version 1.19.2                        

LoomExperiment

                   Changes in version 1.10.1                        

NEW FEATURES

BUG FIXES

LRBaseDbi

                    Changes in version 2.4.0                        

m6Aboost

             Changes in version 0.99.0 (2021-05-27)                 

Maaslin2

                    Changes in version 1.7.1                        

maftools

                    Changes in version 3.14                         

NEW FUNCTIONS

BUG FIXES

ENHANCEMENTS

marr

                    Changes in version 3.13                         

MatrixGenerics

                    Changes in version 1.5.4                        

MatrixQCvis

             Changes in version 1.1.2 (2021-09-06)                  

matter

             Changes in version 1.19.1 (2021-10-20)                 

BUG FIXES

megadepth

                    Changes in version 1.3.3                        

SIGNIFICANT USER-VISIBLE CHANGES

memes

                    Changes in version 1.1.3                        

MeSHDbi

                   Changes in version 1.30.0                        

meshes

                   Changes in version 1.19.3                        

meshr

                    Changes in version 2.0.0                        

metabCombiner

                    Changes in version 1.3.2                        

Changes to labelRows

Changes to metabCombiner

Changes to fit_gam()/ fit_loess

Changes to metabCombiner() & combinedTable / featdata slots

Changes to calcScores() / evaluateParams() / labelRows

Changes to write2file

MetaboCoreUtils

                     Changes in version 1.1                         

MetaboCoreUtils 1.1.1

metaseqR2

             Changes in version 1.5.1 (2021-06-14)                  

NEW FEATURES

BUG FIXES

methylclock

                   Changes in version 0.99.27                       

MetNet

             Changes in version 1.11.5 (2021-10-12)                 

mia

              Changes in version 1.1 (2021-06-04)                   

miaSim

             Changes in version 0.99.0 (2021-09-29)                 

miaViz

                     Changes in version 1.1                         

microbiome

             Changes in version 2.1.2 (2020-07-01)                  

microbiomeMarker

             Changes in version 0.99.0 (2021-09-01)                 

MicrobiomeProfiler

                   Changes in version 0.99.0                        

MicrobiotaProcess

                    Changes in version 1.5.9                        

midasHLA

                    Changes in version 1.1.0                        

miloR

             Changes in version 1.1.0 (2021-10-12)                  

minfi

                    Changes in version 1.39                         

miQC

             Changes in version 1.1.5 (2021-08-24)                  

mirTarRnaSeq

             Changes in version 1.1.3 (2021-08-22)                  

mistyR

                    Changes in version 1.2.0                        

IMPORTANT: R2 is now reported in percentages for intra, multi and gain. Collecting results from running mistyR < 1.1.11 will lead to miscalcuation of gain.R2. Update the performance.txt files by multiplying the values in columns intra.R2 and multi.R2 by 100.

                    Changes in version 1.0.3                        

mixOmics

                   Changes in version 6.18.0                        

new features / enhancements / changes

bug fixes

monaLisa

                   Changes in version 0.99.5                        

mosbi

                    Changes in version 1.0.0                        

Major changes

motifStack

                   Changes in version 1.37.5                        

MQmetrics

                    Changes in version 1.1.8                        

msa

                   Changes in version 1.25.3                        

MsBackendMassbank

                     Changes in version 1.1                         

Changes in 1.1.4

Changes in 1.1.3

Changes in 1.1.2

Changes in 1.1.1

MsBackendMgf

                     Changes in version 1.1                         

Changes in 1.1.3

Changes in 1.1.2

Changes in 1.1.1

MsBackendRawFileReader

                    Changes in version 1.0.0                        

msImpute

                    Changes in version 1.3.0                        

MSnbase

                    Changes in version 2.19                         

Changes in 2.19.2

Changes in 2.19.1

msPurity

                   Changes in version 1.19.2                        

msqrob2

                    Changes in version 1.1.1                        

MSstatsConvert

                    Changes in version 1.2.1                        

MSstatsTMT

             Changes in version 2.2.3 (2021-10-06)                  

MultiAssayExperiment

                   Changes in version 1.20.0                        

Bug fixes and minor improvements

multiHiCcompare

             Changes in version 2.0.0 (2020-11-23)                  

MungeSumstats

                   Changes in version 1.1.27                        

Bug fixes

New Features

New Features

New Features

New Features

Bug fixes

New Features

New Features

Bug fixes

Bug fixes

muscat

                    Changes in version 1.7.2                        

musicatk

             Changes in version 1.3.1 (2021-10-10)                  

mzR

                   Changes in version 2.27.1                        

NanoMethViz

                    Changes in version 2.0.0                        

NanoStringNCTools

             Changes in version 1.1.2 (2020-09-28)                  

NanoTube

                   Changes in version 0.99.0                        

nearBynding

                    Changes in version 1.3.3                        

Changes

Changes

netDx

                    Changes in version 1.5.3                        

netresponse

             Changes in version 1.53.2 (2021-07-28)                 

ngsReports

                    Changes in version 1.9.3                        

normr

                   Changes in version 1.18.2                        

nullranges

                    Changes in version 1.0.0                        

NxtIRFcore

            Changes in version 0.99.12 (2021-10-26)                 

ODER

                   Changes in version 0.99.0                        

NEW FEATURES

OmnipathR

                    Changes in version 3.2.0                        

OncoSimulR

             Changes in version 3.1.2 (2021-10-06)                  

openCyto

                    Changes in version 3.11                         

Enhancements

Bug Fixes

API Changes

Simple renaming

Bug Fixes

oposSOM

                   Changes in version 2.11.1                        

ORFik

                   Changes in version 1.13.7                        

SIGNIFICANT USER-VISIBLE CHANGES

orthogene

                   Changes in version 0.99.9                        

New Features

Fixes

New Features

New Features

Fixes

Fixes

New Features

Fixes

New Features

padma

              Changes in version 1.3 (2021-10-14)                   

pairkat

             Changes in version 0.99.0 (2021-09-21)                 

pcaExplorer

                   Changes in version 2.20.0                        

Other notes

PCAtools

                    Changes in version 2.6.0                        

peakPantheR

             Changes in version 1.7.1 (2021-06-21)                  

pengls

                    Changes in version 0.1.0                        

PharmacoGx

                    Changes in version 2.5.3                        

philr

                   Changes in version 1.19.1                        

USER-VISIBLE CHANGES

INTERNAL

PhIPData

             Changes in version 1.1.1 (2021-08-05)                  

PhosR

                    Changes in version 1.2.1                        

PhyloProfile

                    Changes in version 1.7.8                        

Pigengene

            Changes in version 1.19.50 (2021-10-14)                 

New functions

Bug Fixes

New functions

Bug Fixes

Changes in existing functions

Bug Fixes

plgem

                   Changes in version 1.65.1                        

plotgardener

                   Changes in version 0.99.11                       

BUG FIXES

o : added back to readHic for strawr region parsing. o plotHicSquare subsetting fixed for off diagonal regions.

NEW FEATURES

o All Hi-C functions now allow input of remote Hi-C files.

                   Changes in version 0.99.9                        

This package was previously called BentoBox.

                   Changes in version 0.99.0                        

NEW FEATURES

o Version bump to 0.99.0 for Bioconductor package submission. o bb_mapColors function for users to map a vector to a palette of colors. o linecolor parameter in bb_plotPairs, bb_plotPairsArches, and bb_plotRanges now accepts a single value, a vector of colors, a colorby object, or the value “fill”.

                  Changes in version 0.0.0.14                       

BUG FIXES

o R version requirement changed to (R >= 4.1.0) for proper plot placement.

NEW FEATURES

o colorby object now has a scalePerRegion parameter to scale numerical colorby data to the range of data in a plotted genomic region.

                  Changes in version 0.0.0.13                       

SIGNIFICANT USER-VISIBLE CHANGES

o bb_plotManhattan fill paramete now accepts a single value, a vector of colors, or a colorby object.

                  Changes in version 0.0.0.12                       

SIGNIFICANT USER-VISIBLE CHANGES

o colorby constructor now includes optional palette specification. o bb_plotPairs, bb_plotPairsArches, and bb_plotRanges fill parameter now accepts a single value, a vector of colors, or a colorby object.

BUG FIXES

o GInteractions assembly match checking moved before dataframe conversion.

                  Changes in version 0.0.0.11                       

SIGNIFICANT USER-VISIBLE CHANGES

o Data moved to plotgardenerData package. o Default genome assembly updated to “hg38”.

BUG FIXES

o Streamlined parameter parsing and data reading logic.

                  Changes in version 0.0.0.10                       

NEW FEATURES

o Added unit tests with testthat. o bb_annoDomains function addition. o bb_plotSignal vertical orientation.

                   Changes in version 0.0.0.9                       

NEW FEATURES

o Added a NEWS file to track changes to the package.

BUG FIXES

o Updated viewport parsing for package grid version 4.1.0.

PoDCall

             Changes in version 1.1.1 (2021-06-09)                  

podkat

                   Changes in version 1.25.1                        

polyester

                   Changes in version 1.99.3                        

preciseTAD

             Changes in version 1.3.3 (2021-09-28)                  

proActiv

                    Changes in version 1.3.3                        

procoil

                   Changes in version 2.21.1                        

progeny

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

Major update with the following main points:

pRoloc

                    Changes in version 1.33                         

ProteoDisco

                     Changes in version 1.0                         

ProtGenerics

                   Changes in version 1.25.1                        

psichomics

                   Changes in version 1.20.0                        

ShinyProxy support

Bug fixes

ptairMS

             Changes in version 1.1.4 (2021-09-23)                  

PureCN

                    Changes in version 2.0.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUGFIXES

qcmetrics

                    Changes in version 1.31                         

qcmetrics 1.31.1

QDNAseq

             Changes in version 1.29.6 (2021-10-23)                 

BUG FIXES

PERFORMANCE

MISCELLANEOUS

DOCUMENTATION

DEPRECATION AND DEFUNCT

NEW FEATURES

SOFTWARE QUALITY

BUG FIXES

KNOWN ISSUES

SOFTWARE QUALITY

BUG FIXES

SOFTWARE QUALITY

QFeatures

                    Changes in version 1.3.0                        

QFeatures 1.3.6

QFeatures 1.3.5

QFeatures 1.3.4

QFeatures 1.3.3

QFeatures 1.3.2

QFeatures 1.3.1

QFeatures 1.3.0

qsmooth

             Changes in version 1.9.2 (2021-09-01)                  

QuasR

                   Changes in version 1.34.0                        

USER-VISIBLE CHANGES

RaggedExperiment

                   Changes in version 1.18.0                        

New features

Bug fixes and minor improvements

ramr

             Changes in version 1.1.2 (2021-05-28)                  

rawrr

              Changes in version 1.1 (2021-05-31)                   

RCy3

                   Changes in version 2.14.0                        

ReactomeGSA

             Changes in version 1.7.5 (2021-09-28)                  

recount

                   Changes in version 1.19.2                        

BUG FIXES

recount3

                    Changes in version 1.3.9                        

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

RegEnrich

                    Changes in version 1.3.1                        

rfaRm

             Changes in version 1.5.3 (2021-08-04)                  

RGMQL

                   Changes in version 1.12.2                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

rhdf5

                   Changes in version 2.38.0                        

NEW FEATURES

CHANGES

BUG FIXES

Rhdf5lib

                    Changes in version 1.16                         

Bug fixes

RLSeq

                   Changes in version 0.99.11                       

Package

Status

Pre-release. This version is prior to the first official release (v1.0.0), anticipated in Oct. 2021.

rmspc

                   Changes in version 0.99.0                        

RNAmodR

             Changes in version 1.7.1 (2021-07-27)                  

rols

                    Changes in version 2.21                         

CHANGES IN VERSION 2.21.1

CHANGES IN VERSION 2.21.0

ROSeq

                   Changes in version 1.99.01                       

RPA

             Changes in version 1.49.1 (2021-07-28)                 

rpx

                     Changes in version 2.1                         

rpx 2.1.12

rpx 2.1.11

rpx 2.1.10

rpx 2.1.9

rpx 2.1.8

rpx 2.1.7

rpx 2.1.6

rpx 2.1.5

rpx 2.1.4

rpx 2.1.3

rpx 2.1.2

rpx 2.1.1

rrvgo

                    Changes in version 1.5.4                        

Rsamtools

                    Changes in version 2.10                         

DEPRECATED AND DEFUNCT

RTCGAToolbox

                   Changes in version 2.24.0                        

Bug fixes and minor improvements

rWikiPathways

                   Changes in version 1.14.0                        

S4Vectors

                   Changes in version 0.32.0                        

SIGNIFICANT USER-VISIBLE CHANGES

scanMiR

            Changes in version 0.99.25 (2021-06-25)                 

scater

                   Changes in version 1.22.0                        

scDblFinder

             Changes in version 1.7.3 (2021-07-26)                  

scone

             Changes in version 1.17.1 (2021-07-21)                 

SCOPE

                    Changes in version 1.5.2                        

scp

                    Changes in version 1.3.3                        

scPCA

             Changes in version 1.7.3 (2021-10-07)                  

scReClassify

                   Changes in version 0.99.8                        

scShapes

                    Changes in version 0.1.0                        

scTensor

                    Changes in version 2.4.0                        

segmenter

                   Changes in version 0.99.00                       

selectKSigs

                    Changes in version 1.5.1                        

seqcombo

                   Changes in version 1.15.1                        

sigFeature

                   Changes in version 1.11.2                        

New functionality

signatureSearch

             Changes in version 1.7.3 (2021-08-24)                  

signeR

                   Changes in version 1.19.1                        

singleCellTK

             Changes in version 2.3.2 (2021-10-24)                  

sitePath

                    Changes in version 1.9.4                        

snifter

             Changes in version 1.4.0 (2021-09-09)                  

sparrow

                     Changes in version 1.0                         

Enhancements

Breaking Changes from Pre-release

SpatialDecon

             Changes in version 1.3.0 (2021-09-28)                  

SpatialExperiment

             Changes in version 1.3.2 (2021-07-27)                  

spatialHeatmap

             Changes in version 1.99.0 (2021-10-14)                 

spatzie

                   Changes in version 0.99.7                        

Spectra

                     Changes in version 1.3                         

Changes in 1.3.11

Changes in 1.3.10

Changes in 1.3.9

Changes in 1.3.8

Changes in 1.3.7

Changes in 1.3.6

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

spiky

                    Changes in version 0.1.0                        

splatter

             Changes in version 1.18.0 (2021-10-27)                 

• Added functionality to simulate directly from empirical values

• Added eqtl.coreg parameter to splatPop

• Fixed a bug where too many cells were simulated in splatPop with multiple batches

• Fixed duplicate cell names in splatPopSimulate

SplicingFactory

                    Changes in version 1.0.3                        

statTarget

                     Changes in version 2.0                         

NEW FEATURES

struct

                    Changes in version 1.5.3                        

structToolbox

                    Changes in version 1.5.7                        

SummarizedExperiment

                   Changes in version 1.24.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

surfaltr

             Changes in version 0.99.6 (2021-10-25)                 

svaNUMT

             Changes in version 0.99.0 (2021-04-28)                 

svaRetro

             Changes in version 0.99.0 (2021-04-28)                 

synapsis

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

Changes:

synapter

                    Changes in version 2.17                         

Changes in version 2.17.3

Changes in version 2.17.2

Changes in version 2.17.1

SynExtend

                    Changes in version 1.5.4                        

systemPipeShiny

                   Changes in version 1.3.15                        

New Feature

Minor Change

Bug Fix

New Feature

Major Change

Minor Change

Bug Fix

tanggle

                    Changes in version 0.99                         

NEW FEATURES

TAPseq

             Changes in version 1.5.1 (2021-08-27)                  

TargetSearch

                   Changes in version 1.50.0                        

NEW FEATURES

BUG FIXES

TBSignatureProfiler

                    Changes in version 1.5.0                        

Bug Fixes

Major Changes

Minor Changes

                   Changes in version 2.21.1                        

TCGAutils

                   Changes in version 1.14.0                        

Minor changes and bug fixes

TOAST

                    Changes in version 1.6.1                        

topdownr

                    Changes in version 1.15                         

Changes in version 1.15.1

ToxicoGx

                    Changes in version 1.3.4                        

trackViewer

                   Changes in version 1.29.8                        

transformGamPoi

                     Changes in version 0.1                         

transomics2cytoscape

                    Changes in version 1.2.2                        

BUG FIX

SIGNIFICANT USER-VISIBLE CHANGES

TreeAndLeaf

                    Changes in version 1.5.1                        

treeio

                   Changes in version 1.17.2                        

TRESS

             Changes in version 0.1.0 (2021-07-03)                  

tripr

             Changes in version 0.99.0 (2021-08-15)                 

TVTB

             Changes in version 1.19.1 (2021-08-30)                 

Bug fix

txcutr

                   Changes in version 0.99.0                        

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

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

universalmotif

                   Changes in version 1.12.0                        

NEW FEATURES

MINOR CHANGES

BUG FIXES

BUG FIXES

VAExprs

             Changes in version 0.99.0 (2021-06-07)                 

velociraptor

                    Changes in version 1.3.1                        

veloviz

                 Changes in version 0.0.0.9000                      

ViSEAGO

                     Changes in version 1.7                         

vissE

                    Changes in version 1.2.0                        

weitrix

                    Changes in version 1.5.1                        

wppi

             Changes in version 1.1.3 (2021-10-05)                  

xcms

                   Changes in version 3.15.5                        

zellkonverter

                    Changes in version 1.4.0                        

NEWS from new and existing Data Experiment Packages

benchmarkfdrData2019

             Changes in version 1.7.1 (2021-06-18)                  

BioImageDbs

                    Changes in version 1.0.2                        

NEW FEATURES

NEW FEATURES

bodymapRat

             Changes in version 1.9.1 (2021-06-18)                  

curatedMetagenomicData

                    Changes in version 3.2.0                        

curatedTBData

             Changes in version 0.99.4 (2021-10-18)                 

depmap

            Changes in version 1.7.1                  

dorothea

             Changes in version 1.5.2 (2021-10-13)                  

easierData

                   Changes in version 0.99.0                        

imcdatasets

             Changes in version 1.1.1 (2021-05-25)                  

LRcellTypeMarkers

                    Changes in version 3.13                         

microbiomeDataSets

             Changes in version 1.1.5 (2021-09-08)                  

msigdb

                    Changes in version 1.2.0                        

mtbls2

                   Changes in version 1.23.4                        

NxtIRFdata

             Changes in version 0.99.3 (2021-09-27)                 

ptairData

             Changes in version 1.1.1 (2021-03-05)                  

RforProteomics

                   Changes in version 1.31.1                        

RLHub

                   Changes in version 0.99.6                        

RnBeads.mm10

                    Changes in version 2.1.1                        

scATAC.Explorer

                   Changes in version 0.99.3                        

scpdata

                    Changes in version 1.1.1                        

SingleCellMultiModal

                    Changes in version 1.6.0                        

New features

Bug fixes and minor improvements

spatialDmelxsim

                   Changes in version 0.99.9                        

TabulaMurisSenisData

                   Changes in version 0.99.1                        

TMExplorer

                    Changes in version 1.2.1                        

tuberculosis

                    Changes in version 1.0.0                        

NEWS from new and existing Workflows

GeoMxWorkflows

                   Changes in version 0.99.4                        

NEW FEATURES

NEWS from new and existing books

No new NEWS to report

Deprecated and Defunct Packages

Forty seven software packages were removed from this release (after being deprecated in Bioc 3.13): AffyExpress, affyQCReport, AnnotationFuncs, ArrayTools, bigmemoryExtras, BiocCaseStudies, CancerMutationAnalysis, ChIPSeqSpike, CompGO, CoRegFlux, CrossICC, cytofast, DBChIP, dexus, EasyqpcR, EDDA, eisa, ELBOW, ExpressionView, FlowRepositoryR, genoset, HCABrowser, HCAExplorer, HCAMatrixBrowser, Imetagene, mdgsa, metagenomeFeatures, methyAnalysis, MSEADbi, OutlierD, pcot2, PCpheno, Polyfit, POST, RchyOptimyx, RDAVIDWebService, RNAither, RNAprobR, rnaSeqMap, SAGx, samExploreR, seqplots, simulatorZ, SSPA, ToPASeq, XBSeq, yaqcaffy

Please note: CexoR and IntramiRExploreR, previously announced as deprecated in 3.13, fixed their packages and remained in Bioconductor.

Twenty three software packages are deprecated in this release and will be removed in Bioc 3.15: affyPara, ALPS, alsace, BrainStars, destiny, dualKS, ENCODExplorer, ENVISIONQuery, FindMyFriends, GeneAnswers, gramm4R, KEGGprofile, MouseFM, MSGFgui, MSGFplus, MSstatsTMTPTM, PanVizGenerator, predictionet, RGalaxy, scClassifR, slinky, SRGnet, SwimR

Eleven experimental data packages were removed this release (after being deprecated in BioC 3.13): ceu1kg, ceu1kgv, ceuhm3, cgdv17, dsQTL, facsDorit, gskb, hmyriB36, JctSeqData, MAQCsubsetAFX, yri1kgv

Five experimental data packages are deprecated in this release and will be removed in Bioc 3.15: ABAData, brainImageRdata, PCHiCdata, RITANdata, tcgaWGBSData.hg19

Ninety annotation packages were removed from this release (after being deprecated in Bioc 3.13): 12 LRBase.XXX.eg.db packages (replaced with AHLRBaseDbs), MafDb.gnomAD.r3.0.GRCh38, MafH5.gnomAD.r3.0.GRCh38, 73 MeSH.XXX.eg.db packages (replaced with AHMeSHDbs), greengenes13.5MgDb, ribosomaldatabaseproject11.5MgDb, silva128.1MgDb

One annotation package was deprecated in this release and will be removed in Bioc 3.15: org.Pf.plasmo.db

One workflow package was removed from this release (after being deprecated in Bioc 3.13): eQTL

No workflow packages were deprecated in this release.