October 28, 2020

Bioconductors:

We are pleased to announce Bioconductor 3.12, consisting of 1974 software packages, 398 experiment data packages, 968 annotation packages, and 28 workflows.

There are 125 new software packages, 9 new data experiment packages, 2 new annotation packages, 1 new workflow, 2 online books, and many updates and improvements to existing packages; Bioconductor 3.12 is compatible with R 4.0.3, and is supported on Linux, 32- and 64-bit Windows, and macOS 10.14.6 Mojave or higher. This release will include an updated Bioconductor Amazon Machine Image and Docker containers.

Thank you to everyone for your contribution to Bioconductor

Visit Bioconductor BiocViews for details and downloads.

Contents

Getting Started with Bioconductor 3.12

To update to or install Bioconductor 3.12:

  1. Install R 4.0.3. Bioconductor 3.12 has been designed expressly for this version of R.

  2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 125 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 two new annotation packages in this release of Bioconductor.

New Workflow Packages

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

New Online Books

There are 2 online books in this release of Bioconductor. While the OSCA book has been around for a longer period of time than this release, this is the first release where the book is being hosted, built. and checked by the Bioconductor builders.

NEWS from new and existing Software Packages

a4

                   Changes in version 1.37.2                        

a4Base

                   Changes in version 1.37.3                        

a4Classif

                   Changes in version 1.37.1                        

a4Core

                   Changes in version 1.37.1                        

a4Preproc

                   Changes in version 1.37.1                        

a4Reporting

                   Changes in version 1.37.1                        

ADImpute

                    Changes in version 2.1.0                        

AffiXcan

                    Changes in version 1.7.1                        

BUG FIXED

aggregateBioVar

             Changes in version 0.99.0 (2020-09-03)                 

alevinQC

                    Changes in version 1.5.2                        

AlphaBeta

             Changes in version 1.2.3 (2020-06-06)                  

AlpsNMR

             Changes in version 2.99.5 (2020-10-14)                 

Breaking changes

Other changes

ANCOMBC

             Changes in version 0.99.5 (2020-10-19)                 

AnnotationHub

                   Changes in version 2.21.0                        

BUG FIX

USER-VISIBLE MODIFICATIONS

AnnotationHubData

                   Changes in version 1.19.0                        

INTERNAL BUG CORRECTION

annotatr

                   Changes in version 1.16.0                        

USER-FACING CHANGES

BUGFIXES

AnVIL

                    Changes in version 1.2.0                        

NEW FEATURES

AnVILBilling

                   Changes in version 0.0.12                        

AnVILPublish

                   Changes in version 0.0.10                        

APAlyzer

             Changes in version 1.3.3 (2020-07-20)                  

artMS

             Changes in version 1.6.7 (2020-10-22)                  

ASpli

                   Changes in version 1.99.3                        

NEW FUNCTIONS AND FUNCTIONALITIES

NEW FUNCTIONS AND FUNCTIONALITIES

FUNCTIONS DEPRECATED

AssessORF

             Changes in version 1.7.1 (2020-10-23)                  

ATACseqQC

                   Changes in version 1.13.9                        

Autotuner

             Changes in version 1.3.0 (2020-09-24)                  

BANDITS

                    Changes in version 1.4.1                        

BASiCS

             Changes in version 2.1.16 (2020-10-22)                 

basilisk

                    Changes in version 1.2.0                        

basilisk.utils

                    Changes in version 1.2.0                        

batchelor

                    Changes in version 1.6.0                        

BayesSpace

                   Changes in version 0.99.8                        

Minor improvements and fixes

Minor improvements and fixes

New features

Minor improvements and fixes

Minor improvements and fixes

New features

Minor improvements and fixes

Minor improvements and fixes

Minor improvements and fixes

Minor improvements and fixes

New features

BgeeCall

                    Changes in version 1.5.3                        

BgeeDB

                   Changes in version 2.14.1                        

bigPint

             Changes in version 1.5.1 (2020-08-23)                  

plotClusters() function now has option for superimposing pairs or whole data using the showPairs parameter.

BiocCheck

                    Changes in version 1.25                         

DEPRECATION ANNOUNCEMENT

NEW FEATURES

BUG FIXES

USER SIGNIFICANT CHANGES

BiocParallel

                    Changes in version 1.24                         

BUG FIXES

BiocSet

                     Changes in version 1.3                         

BUG FIX

NEW FEATURES

BiocSingular

                    Changes in version 1.6.0                        

biocthis

                   Changes in version 0.99.0                        

NEW FEATURES

biocViews

                   Changes in version 1.57.0                        

NEW FEATURES

BUG FIX

biomaRt

                   Changes in version 2.46.0                        

BUG FIXES

BioMM

                    Changes in version 1.5.7                        

biosigner

                   Changes in version 1.17.2                        

MINOR MODIFICATION

BrainSABER

             Changes in version 0.99.0 (2020-02-14)                 

breakpointR

                    Changes in version 1.7.2                        

BRGenomics

                    Changes in version 1.1.3                        

BridgeDbR

                   Changes in version 1.99.1                        

BUG FIXES

BUG FIXES

SIGNIFICANT USER-LEVEL CHANGES

CAGEr

                   Changes in version 1.31.4                        

BUG FIXES

BUG FIXES

BUG FIXES

CAMERA

                   Changes in version 1.45.2                        

BUG FIXES

Cardinal

             Changes in version 2.7.2 (2020-10-21)                  

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

cbaf

             Changes in version 1.12.0 (2020-04-08)                 

New Features

cBioPortalData

                    Changes in version 2.2.0                        

New features

Bug fixes and minor improvements

CellaRepertorium

             Changes in version 0.99.0 (2020-09-28)                 

Submitted to bioconductor.

CellTrails

                    Changes in version 1.7.1                        

CeTF

                    Changes in version 1.0.2                        

cfDNAPro

                   Changes in version 0.99.1                        

ChAMP

                   Changes in version 2.18.2                        

Chicago

             Changes in version 1.17.1 (2020-09-08)                 

ChIPpeakAnno

                   Changes in version 3.23.12                       

ChIPQC

                   Changes in version 1.25.1                        

ChromSCape

             Changes in version 0.99.0 (2020-10-23)                 

chromstaR

                   Changes in version 1.14.2                        

BUG FIXES

BUG FIXES

CHRONOS

                   Changes in version 1.17.2                        

circRNAprofiler

                    Changes in version 1.3.1                        

Added files to fix bugs

cleanUpdTSeq

                   Changes in version 1.27.1                        

cleaver

             Changes in version 1.27.1 (2020-06-05)                 

clusterProfiler

                   Changes in version 3.17.5                        

clustifyr

             Changes in version 1.1.2 (2020-09-21)                  

CNVPanelizer

                   Changes in version 1.21.2                        

cola

                    Changes in version 1.5.5                        

ComplexHeatmap

                    Changes in version 2.5.6                        

CoreGx

                    Changes in version 1.1.5                        

CRISPRseek

                   Changes in version 1.29.2                        

csaw

                   Changes in version 1.24.0                        

cTRAP

                     Changes in version 1.8                         

Interactive functions for loading data and analysing results

Major changes

Bug fixes and minor changes

customCMPdb

             Changes in version 1.1.0 (2020-10-02)                  

cytomapper

             Changes in version 1.1.6 (2020-10-23)                  

CytoML

                    Changes in version 3.11                         

API Changes

Fixes/internal changes

API Changes

Fixes/internal changes

CytoTree

             Changes in version 0.99.6 (2020-06-19)                 
                   Changes in version 1.27.9                        

DAMEfinder

                    Changes in version 1.1.3                        

dasper

                   Changes in version 0.99.2                        

NEW FEATURES

NEW FEATURES

NEW FEATURES

decompTumor2Sig

             Changes in version 2.4.1 (2020-07-27)                  

deepSNV

             Changes in version 1.99.3 (2013-07-25)                 

Updates

Bugfixes

Updates

Bugfixes

Updates

Bugfixes

Updates

DegNorm

                   Changes in version 0.99.13                       

SUBMIT TO BIOCONDUCTOR FOR REVIEW

DEGreport

                   Changes in version 1.25.1                        

DelayedArray

                   Changes in version 0.16.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

DelayedMatrixStats

                   Changes in version 1.12.0                        

DeMixT

                    Changes in version 1.6.0                        

densvis

             Changes in version 0.99.0 (2020-09-24)                 

DepecheR

             Changes in version 1.5.4 (2020-09-17)                  

DESeq2

                   Changes in version 1.30.0                        

DEWSeq

             Changes in version 1.3.0 (2020-09-30)                  

DIAlignR

                    Changes in version 1.1.5                        

DiffBind

                     Changes in version 3.0                         

The main upgrade involves how the modelling and normalization are done. DiffBind now supports models and contrasts of arbitrary complexity using either/both DESeq2 or/and edgeR, as well as a myriad of normalization options.

NB:

The previous methods for modelling are maintained for backward compatibility, however they are not the default. To repeat earlier analyses, dba.contrast() must be called explicitly with design=FALSE. See ?DiffBind3 for more information.

The default mode for dba.count() is now to center around summits (resulting in 401bp intervals). To to avoid recentering around summits as was the previous default, set summits=FALSE (or to a more appropriate value).

Normalization options have been moved from dba.analyze() to the new interface function dba.normalize(). Any non-default normalization options must be specified using dba.normalize().

Director

             Changes in version 1.15.1 (2020-10-04)                 

DiscoRhythm

             Changes in version 1.5.6 (2020-07-22)                  

distinct

                    Changes in version 1.0.3                        

dittoSeq

                     Changes in version 1.2                         

DMCFB

                    Changes in version 1.3.1                        

New Features

Removed

DMCHMM

                   Changes in version 1.11.1                        

CHANGES

BUG FIX

DOSE

                   Changes in version 3.15.4                        

drawProteins

                    Changes in version 1.9.0                        

DropletUtils

                   Changes in version 1.10.0                        

easyRNASeq

                   Changes in version 2.25.1                        

EDASeq

                   Changes in version 2.23.1                        

edgeR

                   Changes in version 3.32.0                        

EnhancedVolcano

                     Changes in version 1.8                         

ENmix

                   Changes in version 1.25.9                        

EnrichmentBrowser

                   Changes in version 2.20.0                        

enrichplot

                    Changes in version 1.9.5                        

ensemblVEP

                   Changes in version 1.32.0                        

epivizrServer

                   Changes in version 999.999                       

escape

                   Changes in version 0.99.9                        

ExperimentHub

                   Changes in version 1.15.0                        

BUG FIXES

USER-VISIBLE CHANGES

ExperimentSubset

             Changes in version 0.99.0 (2020-10-02)                 

PRE-RELEASE

ExploreModelMatrix

                    Changes in version 1.1.4                        

FamAgg

                   Changes in version 1.17.1                        

famat

             Changes in version 0.99.9 (2020-10-26)                 

FGNet

                    Changes in version 3.23                         

fgsea

                   Changes in version 1.15.2                        

FilterFFPE

             Changes in version 0.99.3 (2020-10-08)                 

fishpond

                    Changes in version 1.6.0                        

flowCut

                    Changes in version 1.0.0                        

NEW FEATURES

BUG FIXES

flowFP

                   Changes in version 1.47.0                        

flowSpecs

             Changes in version 1.3.3 (2020-09-03)                  

fmrs

                   Changes in version 0.99.3                        

IMPROVEMENTS SINCE LAST RELEASE

BUG FIXES

FRASER

                    Changes in version 1.1.6                        

FScanR

             Changes in version 0.99.7 (2020-09-08)                 

gage

                   Changes in version 2.39.3                        

GAPGOM

             Changes in version 1.5.1 (2020-07-01)                  

Changed

GCSConnection

                    Changes in version 1.1.6                        

gdsfmt

                   Changes in version 1.24.1                        

UTILITIES

GENESIS

                   Changes in version 2.19.7                        

GeneTonic

                    Changes in version 1.2.0                        

New features

Other notes

GenomeInfoDb

                   Changes in version 1.26.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

genomeIntervals

                   Changes in version 1.45.2                        

GenomicFeatures

                   Changes in version 1.42.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

GenomicOZone

                    Changes in version 1.3.1                        

GenomicRanges

                   Changes in version 1.42.0                        

NEW FEATURES

getDEE2

                   Changes in version 0.99.16                       

ggtree

                    Changes in version 2.3.7                        

ggtreeExtra

                   Changes in version 0.99.0                        

the 0.99.0 or 0.99.x version mean I am submitting it to Bioconductor. (20200710, Fri)

0.99.9

0.99.10

0.99.11

0.99.12

0.99.13

0.99.14

0.99.15

0.99.16

0.99.17

0.99.18

0.99.19

Glimma

                    Changes in version 2.0.0                        

glmGamPoi

                     Changes in version 1.1                         

GNET2

                    Changes in version 1.5.5                        

GOSemSim

                   Changes in version 2.15.2                        

GPA

                    Changes in version 1.1.0                        

graphite

             Changes in version 1.35.2 (2020-10-12)                 

GreyListChIP

                   Changes in version 1.22.0                        

GSEAmining

                   Changes in version 0.99.0                        

GSgalgoR

             Changes in version 0.99.3 (2020-10-23)                 

Gviz

                   Changes in version 1.33.1                        

NEW FEATURES

BUG FIXES

gwascat

                   Changes in version 2.21.7                        

USER VISIBLE CHANGES

USER VISIBLE CHANGES

GWASTools

                   Changes in version 1.35.2                        

HCAMatrixBrowser

                    Changes in version 1.0.0                        

New features

Bug fixes and minor improvements

HDF5Array

                   Changes in version 1.18.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Herper

             Changes in version 0.99.2 (2020-10-19)                 

HIBAG

                   Changes in version 1.26.0                        

HiCcompare

             Changes in version 1.11.1 (2020-08-14)                 

HPAStainR

             Changes in version 0.99.2 (2020-09-02)                 

hypeR

                   Changes in version 1.05.03                       

ideal

                   Changes in version 1.14.0                        

Other notes

idr2d

                    Changes in version 1.2.2                        

IgGeneUsage

             Changes in version 1.3.3 (2020-10-15)                  

illuminaio

             Changes in version 0.31.1 (2020-07-15)                 

UPDATES

DOCUMENTATION

BUG FIXES

NOTES

ILoReg

             Changes in version 0.99.0 (2020-06-25)                 

immunoClust

                   Changes in version 1.21.2                        

infercnv

             Changes in version 1.5.3 (2020-10-23)                  

Informeasure

             Changes in version 0.99.8 (2020-10-06)                 

intansv

                   Changes in version 1.29.0                        

Notes

IRanges

                   Changes in version 2.24.0                        

NEW FEATURES

DEPRECATED AND DEFUNCT

BUG FIXES

ISAnalytics

            Changes in version 0.99.15 (2020-10-22)                 

NEW FEATURES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

MINOR CHANGES

NEW FEATURES

MINOR FIXES

ISanalytics is officially on bioconductor!

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

MINOR FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

iSEE

                   Changes in version 2.1.27                        

iSEEu

                    Changes in version 1.1.9                        

IsoCorrectoR

                    Changes in version 1.6.2                        

IsoformSwitchAnalyzeR

            Changes in version 1.11.11 (2020-10-13)                 

isomiRs

                   Changes in version 1.17.2                        

FIX

FIX

KEGGprofile

                   Changes in version 1.31.1                        

LACE

                    Changes in version 1.0.1                        

lefser

                    Changes in version 1.0.0                        

limma

                   Changes in version 3.46.0                        

New functionality

Code improvements

Documentation

Bug fixes

lipidr

                     Changes in version 2.4                         

LRBaseDbi

                    Changes in version 2.0.0                        

Maaslin2

                    Changes in version 1.3.2                        

maftools

                    Changes in version 3.12                         

BUG REPORTS

ENHANCEMENTS

NEW FUNCTIONS

DEPRECATED

MAGeCKFlute

                    Changes in version 1.9.1                        

marr

                   Changes in version 0.99.4                        

MatrixGenerics

                    Changes in version 1.2.0                        

matter

                   Changes in version 1.15.1                        

BUG FIXES

megadepth

                   Changes in version 0.99.0                        

NEW FEATURES

MesKit

                   Changes in version 0.99.11                       

Changes

Changes

metabCombiner

             Changes in version 0.99.0 (2020-09-11)                 

metabolomicsWorkbenchR

                   Changes in version 0.99.0                        

metaMS

                   Changes in version 1.25.1                        

MetaNeighbor

                    Changes in version 1.9.1                        

metaseqR2

             Changes in version 1.1.21 (2020-08-05)                 

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

NEW FEATURES

BUG FIXES

MetCirc

             Changes in version 1.19.0 (2020-07-02)                 

MethReg

                    Changes in version 0.1.0                        

methrix

                   Changes in version 1.4.00                        

methylKit

                   Changes in version 1.15.3                        

NEW FUNCTIONS AND FEATURES

IMPROVEMENTS AND BUG FIXES

IMPROVEMENTS AND BUG FIXES

microbiome

             Changes in version 2.1.2 (2020-07-01)                  

microbiomeExplorer

                    Changes in version 1.0.0                        

MicrobiotaProcess

                   Changes in version 1.1.13                        

miRSM

                 Changes in version 1.7.2-1.7.3                     

mitch

                   Changes in version 1.0.12                        

mixOmics

                   Changes in version 6.14.0                        

new features / enhancements / changes

bug fixes

MOFA2

                   Changes in version 0.99.0                        

MOGAMUN

                   Changes in version 0.99.0                        

motifStack

                   Changes in version 1.33.14                       

MouseFM

             Changes in version 0.99.9 (2020-08-23)                 

msa

                   Changes in version 1.21.1                        

MsCoreUtils

                     Changes in version 1.1                         

Changes in 1.1.7

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

Changes in 1.1.0

MSEADbi

                   Changes in version 0.99.0                        

msImpute

                   Changes in version 0.99.26                       

MSnbase

                    Changes in version 2.15                         

Changes in 2.15.7

Changes in 2.15.6

Changes in 2.15.5

Changes in 2.15.4

Changes in 2.15.3

Changes in 2.15.2

Changes in 2.15.1

Changes in 2.15.0

MSPrep

             Changes in version 0.99.0 (2020-10-02)                 

msPurity

                   Changes in version 1.15.1                        

MSstatsConvert

                   Changes in version 0.99.0                        

MSstatsPTM

             Changes in version 0.99.0 (2020-09-28)                 

MSstatsTMT

             Changes in version 1.6.6 (2020-10-13)                  

MSstatsTMTPTM

             Changes in version 0.99.0 (2018-09-21)                 

MultiAssayExperiment

                   Changes in version 1.16.0                        

New features

Bug fixes and minor improvements

multicrispr

             Changes in version 0.99.0 (2020-04-24)                 

multiGSEA

                   Changes in version 0.99.0                        

multiHiCcompare

             Changes in version 1.7.1 (2020-08-28)                  

musicatk

            Changes in version 0.99.10 (2020-10-02)                 

PRE-RELEASE

NanoMethViz

                    Changes in version 1.0.0                        

NBAMSeq

             Changes in version 1.5.1 (2020-05-04)                  

ncRNAtools

             Changes in version 0.99.9 (2020-10-01)                 

Nebulosa

                   Changes in version 0.99.94                       

netDx

                    Changes in version 1.1.4                        

Changes

somatic mutations

NewWave

             Changes in version 0.99.5 (2020-09-08)                 

ngsReports

                    Changes in version 1.5.5                        

Omixer

                    Changes in version 0.99                         

OmnipathR

             Changes in version 1.99.0 (2020-10-03)                 

OncoSimulR

             Changes in version 2.19.2 (2020-06-03)                 

onlineFDR

                    Changes in version 1.8.0                        

MODIFICATIONS

openCyto

                    Changes in version 3.11                         

Enhancements

Bug Fixes

API Changes

Simple renaming

Bug Fixes

OrganismDbi

                   Changes in version 1.32.0                        

BUG FIXES

OUTRIDER

                    Changes in version 1.7.1                        

padma

              Changes in version 0.99                   

pageRank

             Changes in version 0.99.0 (2020-09-21)                 

PAST

             Changes in version 1.4.1 (2020-04-30)                  

pathview

                   Changes in version 1.29.1                        

pcaExplorer

                   Changes in version 2.16.0                        

Other notes

PCAtools

                    Changes in version 2.2.0                        

peakPantheR

             Changes in version 1.3.4 (2020-10-23)                  

PepsNMR

             Changes in version 1.7.1 (2020-07-21)                  

BUG CORRECTION

periodicDNA

                    Changes in version 0.3.2                        

PGA

                   Changes in version 1.19.1                        

phantasus

                    Changes in version 1.9.5                        

PharmacoGx

                   Changes in version 2.1.12                        

PhosR

                    Changes in version 0.1.5                        

PhyloProfile

                   Changes in version 1.3.11                        

Pigengene

            Changes in version 1.15.20 (2020-09-28)                 

Changes in existing functions

Changes in existing functions

Bug Fixes

Changes in existing functions

Bug Fixes

pipeComp

            Changes in version 0.99.43 (2020-07-20)                 

plyranges

                    Changes in version 1.9.3                        
  1. join_nearest_(x, y, …, distance = TRUE) family of functions now takes a new argument, distance, which allows the user to add a column for the distance of the nearest range y to that in x.
  2. add_nearest_distance_(x, y, …) family of functions, which will add a new metadata column to the x ranges object which contains the distance to its nearest neighbor in y. If there are no nearest neighbors, the new column will be given a missing value.

polyester

                   Changes in version 1.99.3                        

POMA

                   Changes in version 0.99.45                       

preciseTAD

             Changes in version 0.99.6 (2020-08-30)                 

proActiv

                   Changes in version 0.99.0                        

proDA

                     Changes in version 1.3                         

progeny

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

Major update with the following main points:

pRolocGUI

                    Changes in version 1.99                         

CHANGES IN VERSION 1.99.2

CHANGES IN VERSION 1.99.1

psichomics

                   Changes in version 1.14.4                        

Support for loading more data formats

New features

Bug fixes and minor changes

Fix unit tests for R 4.0

PureCN

                   Changes in version 1.20.0                        

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUGFIXES

QFeatures

                    Changes in version 0.99                         

QFeatures 0.99.4

QFeatures 0.99.3

QFeatures 0.99.2

QFeatures 0.99.1

QFeatures 0.99.0

qPLEXanalyzer

                    Changes in version 1.7.3                        

QuasR

                   Changes in version 1.30.0                        

NEW FEATURES

RadioGx

                    Changes in version 1.0.1                        

RaggedExperiment

                   Changes in version 1.14.0                        

Bug fixes and minor improvements

randRotation

             Changes in version 1.1.1 (2020-09-23)                  

rBiopaxParser

                   Changes in version 2.29.1                        

RCy3

                   Changes in version 2.10.0                        

ReactomeGSA

             Changes in version 1.3.6 (2020-09-01)                  

reconsi

                    Changes in version 1.1.2                        

recount3

                   Changes in version 0.99.0                        

NEW FEATURES

recountmethylation

                   Changes in version 0.99.0                        

recoup

             Changes in version 1.17.1 (2020-05-03)                 

NEW FEATURES

BUG FIXES

RegEnrich

                   Changes in version 0.99.19                       

regionReport

                   Changes in version 1.23.2                        

SIGNIFICANT USER-VISIBLE CHANGES

regutools

                    Changes in version 1.1.3                        

SIGNIFICANT USER-VISIBLE CHANGES

DOCUMENTATION UPDATES

SIGNIFICANT USER-VISIBLE CHANGES

ResidualMatrix

                    Changes in version 1.0.0                        

rfaRm

             Changes in version 1.1.10 (2020-10-13)                 

rGREAT

                   Changes in version 1.21.1                        

rgsepd

                    Changes in version 1.21                         

rhdf5

                   Changes in version 2.34.0                        

NEW FEATURES

CHANGES

BUG FIXES

rhdf5filters

                    Changes in version 1.2.0                        

BUG FIXES

ribosomeProfilingQC

                    Changes in version 1.1.6                        

RNAAgeCalc

             Changes in version 1.1.2 (2020-09-20)                  

rnaEditr

                   Changes in version 0.99.1                        

2020-10-01

Added rnaEditr.Rproj into .gitignore to fix the building error.

                   Changes in version 0.99.0                        

2020-09-22

We are planning to submit to Bioconductor by this Friday, and here is the link to the issue on gitlab where we resolve BiocCheck() ERRORs, WARNINGs, and NOTEs: https://gitlab.com/Jennyzly2016/rnaEditr/-/issues/64

RNAmodR

             Changes in version 1.3.5 (2020-08-30)                  

RnaSeqSampleSize

             Changes in version 1.99.2 (2020-10-22)                 

BUG FIXES

RnBeads

                    Changes in version 2.7.1                        

rols

                    Changes in version 2.17                         

CHANGES IN VERSION 2.17.4

CHANGES IN VERSION 2.17.3

CHANGES IN VERSION 2.17.2

CHANGES IN VERSION 2.17.1

CHANGES IN VERSION 2.17.0

ROSeq

                   Changes in version 1.99.01                       

rrvgo

                    Changes in version 1.1.3                        

rScudo

                    Changes in version 1.5.1                        

USER VISIBLE CHANGES

rsemmed

                   Changes in version 0.99.0                        

Rsubread

                    Changes in version 2.4.0                        

RTCA

                 Changes in version 2009-07-13                      

RTCGAToolbox

                   Changes in version 2.20.0                        

New features

Bug fixes and minor improvements

Rtpca

             Changes in version 0.99.2 (2020-06-05)                 

rWikiPathways

                   Changes in version 1.10.0                        

S4Vectors

                   Changes in version 0.28.0                        

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

SAIGEgds

                    Changes in version 1.3.3                        

sangeranalyseR

                   Changes in version 0.99.1                        

SCATE

                    Changes in version 1.0.0                        

scCB2

                   Changes in version 0.99.31                       

scDataviz

                    Changes in version 1.0.0                        

scDblFinder

             Changes in version 1.3.25 (2020-10-26)                 

scDD

             Changes in version 1.13.1 (2020-08-17)                 

SCFA

             Changes in version 0.99.0 (2020-08-13)                 

scp

                    Changes in version 0.99                         

scp 0.99.4

scp 0.99.3

scp 0.99.2

scp 0.99.1

scp 0.99.0

scPCA

             Changes in version 1.3.10 (2020-10-16)                 

scran

                   Changes in version 1.18.0                        

scRepertoire

                    Changes in version 1.2.3                        

SUBMITTED

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

scTensor

                    Changes in version 2.0.0                        

scTGIF

                    Changes in version 1.2.1                        

scuttle

                    Changes in version 1.0.0                        

SDAMS

                    Changes in version 1.9.2                        

semisup

             Changes in version 1.14.0 (2020-05-05)                 

SeqArray

                   Changes in version 1.29.2                        

UTILITIES

BUG FIXES

BUG FIXES

SeqGate

             Changes in version 0.99.3 (2020-09-18)                 
                   Changes in version 1.55.2                        

NEW FEATURES

BUG FIXES

SeqVarTools

                   Changes in version 1.27.1                        

sevenbridges

                   Changes in version 1.19.2                        

Improvements

Bug Fixes

Improvements

SharedObject

                   Changes in version 1.3.18                        

ShortRead

                    Changes in version 1.48                         

NEW FEATURES

signatureSearch

             Changes in version 1.2.4 (2020-08-14)                  

simplifyEnrichment

                   Changes in version 0.99.5                        

SingleCellExperiment

                   Changes in version 1.12.0                        

singleCellTK

             Changes in version 2.0.0 (2020-10-16)                  

SingleR

                    Changes in version 1.4.0                        

sitePath

                   Changes in version 1.5.25                        

snifter

             Changes in version 0.99.0 (2020-07-17)                 

SNPRelate

                   Changes in version 1.24.0                        

sparseMatrixStats

             Changes in version 1.0.5 (2020-05-17)                  

SparseSignatures

                    Changes in version 2.0.0                        

SpatialDecon

             Changes in version 0.99.0 (2020-10-02)                 

spatialHeatmap

             Changes in version 0.99.0 (2020-09-21)                 

Spectra

                    Changes in version 0.99                         

Changes in 0.99.11

Changes in 0.99.10

Changes in 0.99.9

Changes in 0.99.8

Changes in 0.99.7

Changes in 0.99.6

Changes in 0.99.5

Changes in 0.99.4

Changes in 0.99.3

Changes in 0.99.2

Changes in 0.99.0

splatter

             Changes in version 1.14.0 (2020-10-28)                 

splineTimeR

             Changes in version 1.17.1 (2020-07-18)                 

SPsimSeq

                   Changes in version 0.99.0                        

statTarget

                     Changes in version 2.0                         

NEW FEATURES

struct

                    Changes in version 1.1.2                        

structToolbox

                    Changes in version 1.1.2                        

SummarizedExperiment

                   Changes in version 1.20.0                        

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

SWATH2stats

                   Changes in version 1.19.3                        

UPDATE

BUG FIXES

NEW FEATURES

update

NEW FEATURES

TADCompare

            Changes in version 0.99.35 (2020-05-15)                 

TargetSearch

                   Changes in version 1.46.0                        

NEW FEATURES

BUG FIXES

SIGNIFICANT USER-VISIBLE CHANGES

TCC

                   Changes in version 1.29.1                        

TCGAutils

                   Changes in version 1.10.0                        

New features

Minor changes and bug fixes

tofsims

                    Changes in version 099.1                        

SIGNIFICANT USER-VISIBLE CHANGES

INTERNALS

tomoda

             Changes in version 0.99.0 (2020-09-15)                 

topconfects

                    Changes in version 1.5.3                        

ToxicoGx

                    Changes in version 1.1.0                        

TPP

                   Changes in version 3.17.6                        

TPP2D

                    Changes in version 1.5.5                        

trackViewer

                   Changes in version 1.25.4                        

tradeSeq

             Changes in version 1.3.19 (2020-10-16)                 

transite

                    Changes in version 1.6.3                        

transomics2cytoscape

                    Changes in version 1.0.0                        

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

treeio

                   Changes in version 1.13.1                        

TRONCO

                   Changes in version 2.21.1                        

TSCAN

                   Changes in version 1.28.0                        

tximeta

                    Changes in version 1.8.0                        

tximport

                   Changes in version 1.18.0                        

UMI4Cats

                   Changes in version 0.99.21                       

IMPORTANT

UPDATES

uncoverappLib

                 Changes in version 0.0.0.9000                      

setup

universalmotif

                    Changes in version 1.8.0                        

NEW FEATURES

MINOR CHANGES

BUG FIXES

BUG FIXES

BUG FIXES

BUG FIXES

BUG FIXES

variancePartition

                   Changes in version 1.19.20                       

VariantAnnotation

                   Changes in version 1.36.0                        

NEW FEATURES

velociraptor

                   Changes in version 0.99.9                        

VERSO

                    Changes in version 1.0.0                        

ViSEAGO

                     Changes in version 1.3                         

VplotR

             Changes in version 0.5.0 (2020-05-25)                  

wavClusteR

                   Changes in version 2.23.0                        

weitrix

                   Changes in version 1.1.10                        

wpm

                   Changes in version 0.99.13                       

xcms

                   Changes in version 3.11.8                        

zellkonverter

                    Changes in version 1.0.0                        

zinbwave

             Changes in version 1.11.6 (2020-07-18)                 

NEWS from new and existing Data Experiment Packages

chipseqDBData

                    Changes in version 1.6.0                        

clustifyrdatahub

             Changes in version 0.99.4 (2020-09-02)                 

curatedTCGAData

                   Changes in version 1.12.0                        

Bug fixes and minor improvements

depmap

                     Changes in version 1.3                         

Changes in version 1.3.2

Changes in version 1.3.1

dorothea

             Changes in version 1.1.2 (2020-10-08)                  

dsQTL

                    Changes in version 2.17                         

USER VISIBLE CHANGES

FieldEffectCrc

             Changes in version 0.99.2 (2020-09-20)                 

MethylSeqData

                    Changes in version 1.0.0                        

pRolocdata

                   Changes in version 1.27.1                        

RegParallel

                    Changes in version 1.8.0                        

RforProteomics

                   Changes in version 1.27.1                        

SCATEData

                    Changes in version 1.0.0                        

scRNAseq

                    Changes in version 2.4.0                        

signatureSearchData

             Changes in version 1.2.1 (2020-08-14)                  

SingleCellMultiModal

                    Changes in version 1.2.0                        

New features

Bug fixes and minor improvements

spatialLIBD

                    Changes in version 1.1.5                        

NEW FEATURES

NEW FEATURES

timecoursedata

             Changes in version 0.99.0 (2020-05-15)                 

TMExplorer

                   Changes in version 0.99.6                        

NEWS from new and existing Workflows

fluentGenomics

                    Changes in version 1.0.1                        

Deprecated and Defunct Packages

Fifty Six software packages were removed from this release (after being deprecated in Bioc 3.11): affypdnn, AnalysisPageServer, anamiR, BayesPeak, bgafun, biosvd, birta, CALIB, CAMTHC, cellGrowth, chroGPS, cobindR, CTDquerier, CVE, DChIPRep, DEDS, DupChecker, FEM, gCMAP, gCMAPWeb, geecc, Genominator, IdMappingAnalysis, IdMappingRetrieval, IPPD, kimod, LMGene, lol, LVSmiRNA, M3D, manta, MaxContrastProjection, MCRestimate, MergeMaid, mitoODE, MoPS, motifRG, MTseeker, nem, PAPi, pcaGoPromoter, pint, plw, PowerExplorer, proteoQC, QUALIFIER, readat, RefNet, RIPSeeker, SANTA, scfind, splicegear, sRAP, triform, Vega, waveTiling

Sixty eight software are deprecated in this release and will be removed in Bioc 3.13: adaptest, ArrayTV, BioSeqClass, CGEN, CHARGE, chimera, CNVtools, CorMut, DESeq, explorase, flowFit, flowSpy, flowType, flowVS, focalCall, FourCSeq, FunciSNP, GeneticsDesign, GenRank, GGBase, GGtools, GOFunction, gQTLBase, gQTLstats, hicrep, ImpulseDE, ImpulseDE2, joda, JunctionSeq, LINC, Logolas, mcaGUI, metaArray, metaseqR, methVisual, methyvim, Mirsynergy, MmPalateMiRNA, MOFA (Please see MOFA2), MotIV, NarrowPeaks, netbenchmark, netReg, OGSA, OmicsMarkeR, pathprint, PathwaySplice, PGA, PGSEA, plrs, prada, Prize, Rariant, reb, Roleswitch, rTANDEM, sampleClassifier, sapFinder, scsR, shinyTANDEM, sigaR, signet, simpleaffy, spotSegmentation, Starr, SVAPLSseq, TxRegInfra, xps

Two experimental data packages were removed this release (after being deprecated in BioC 3.11): MTseekerData, RIPSeekerData

Sixteen experimental data packages are deprecated in this release and will be removed in Bioc 3.13: flowFitExampleData, FunciSNP.data, geuvPack, geuvStore2, GGdata, methyvimData, mitoODEdata, Mulder2012, pathprintGEOData, pcaGoPromoter.Hs.hg19, pcaGoPromoter.Mm.mm9, pcaGoPromoter.Rn.rn4, RNAinteractMAPK, sampleClassifierData, waveTilingData, yriMulti

Nine annotation packages were supposed to be removed this release, however we decided to give an extra cycle for maintainers to adapt and will be removed in 3.13: hom.At.inp.db, hom.Ce.inp.db, hom.Dm.inp.db, hom.Dr.inp.db, hom.Hs.inp.db, hom.Mm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db, KEGG.db.

Five annotation packages are deprecated in this release and will be removed in Bioc 3.13: MeSH.Eco.55989.eg.db, MeSH.Eco.ED1a.eg.db, MeSH.Eco.IAI39.eg.db, MeSH.Eco.UMN026.eg.db, MeSH.Eqc.eg.db (renamed to MeSH.Eca.eg.db)

No workflow packages were removed in this release.

No workflow packages were deprecated in this release.