October 30, 2019

Bioconductors:

We are pleased to announce Bioconductor 3.10, consisting of 1823 software packages, 384 experiment data packages, 953 annotation packages, and 27 workflows.

There are 94 new software packages, 15 new data experiment packages, 3 new annotation packages, and many updates and improvements to existing packages; Bioconductor 3.10 is compatible with R 3.6.1, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. 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 3.10

To update to or install Bioconductor 3.10:

  1. Install R >=3.6.1. Bioconductor 3.10 has been designed expressly for this version of R.

  2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 93 new software packages in this release of Bioconductor.

New Data Experiment Packages

There are 15 new data experiment packages in this release of Bioconductor.

New Annotation Packages

There are 3 new annotation packages in this release of Bioconductor.

NEWS from new and existing Software Packages

AffiXcan

Changes in version 1.3.7

UPDATED VIGNETTE

ALSO MODELS’ P-VALUES AND RHO ARE RETURNED IN CROSS-VALIDATION

Changes in version 1.3.5

P-VALUE OF THE CORRELATION TEST

Changes in version 1.3.3

UPDATED DOCUMENTATION

Changes in version 1.3.2

POPULATION STRUCTURE COVARIATES ARE OPTIONAL

Changes in version 1.3.1

K-FOLD CROSS-VALIDATION IS SUPPORTED

alevinQC

Changes in version 1.1

AlphaBeta

Changes in version 0.99.2 (2019-08-15)

ALPS

Changes in version 0.99.8

Changes in version 0.99.7

Changes in version 0.99.0

AneuFinder

Changes in version 1.12.1

BUG FIXES

AnnotationForge

Changes in version 1.28.0

NEW FEATURES

AnnotationHub

Changes in version 2.17.0

NEW FEATURES

BUG FIXES

AnnotationHubData

Changes in version 1.15.0

MODIFICATIONS

INTERNAL BUG CORRECTION

APAlyzer

Changes in version 0.99.2 (2019-08-18)

Changes in version 0.99.1 (2019-07-14)

apeglm

Changes in version 1.8.0

aroma.light

Changes in version 3.15.1 (2019-08-28)

BUG FIXES

Changes in version 3.15.0 (2019-05-02)

ASpediaFI

Changes in version 0.99.10 (2019-10-25)

Changes in version 0.99.9 (2019-10-22)

Changes in version 0.99.8 (2019-10-17)

Changes in version 0.99.7 (2019-10-17)

Changes in version 0.99.6 (2019-10-16)

Changes in version 0.99.5 (2019-10-15)

Changes in version 0.99.4 (2019-10-01)

Changes in version 0.99.3 (2019-10-01)

Changes in version 0.99.2 (2019-10-01)

Changes in version 0.99.1 (2019-10-01)

Changes in version 0.99.0 (2019-10-01)

AssessORF

Changes in version 1.3.1 (2019-10-22)

ATACseqQC

Changes in version 1.9.9

Changes in version 1.9.8

Changes in version 1.9.7

Changes in version 1.9.6

Changes in version 1.9.5

Changes in version 1.9.4

Changes in version 1.9.3

Changes in version 1.9.2

Changes in version 1.9.1

AUCell

Changes in version 1.7

Autotuner

Changes in version 1.0.1 (2019-07-06)

Changes in version 1.0.0 (2019-07-06)

Changes in version 0.99.9 (2019-08-06)

Changes in version 0.99.8 (2019-08-02)

Changes in version 0.99.7 (2019-08-02)

AWFisher

Changes in version 0.99.2 (2019-06-14)

bamsignals

Changes in version 1.17.3

Changes in version 1.17.2

BANDITS

Changes in version 1.2.0

BASiCS

Changes in version 1.7.20 (2019-10-17)

Changes in version 1.7.19 (2019-10-08)

Changes in version 1.7.18 (2019-10-06)

Changes in version 1.7.17 (2019-10-04)

Changes in version 1.7.16 (2019-10-04)

Changes in version 1.7.15 (2019-09-30)

Changes in version 1.7.14 (2019-09-27)

Changes in version 1.7.13 (2019-09-25)

Changes in version 1.7.12 (2019-09-15)

Changes in version 1.7.11 (2019-09-15)

Changes in version 1.7.10

Changes in version 1.7.9 (2019-09-05)

Changes in version 1.7.8 (2019-08-20)

Changes in version 1.7.7 (2019-08-20)

Changes in version 1.7.6 (2019-08-19)

Changes in version 1.7.5 (2019-07-30)

Changes in version 1.7.4 (2019-07-30)

Changes in version 1.7.3 (2019-07-29)

Changes in version 1.7.2 (2019-07-28)

Changes in version 1.7.1 (2019-07-27)

batchelor

Changes in version 1.2.0

bcSeq

Changes in version 1.7.1

BEclear

Changes in version 2.1.4 (2019-05-17)

Changes in version 2.1.3 (2019-05-13)

Changes in version 2.1.2 (2019-05-10)

Changes in version 2.1.1 (2019-05-09)

BiocNeighbors

Changes in version 1.4.0

BioCor

Changes in version 1.10.1

Changes in version 1.8.1

BiocParallel

Changes in version 1.20

BUG FIXES

BiocSingular

Changes in version 1.2.0

biomaRt

Changes in version 2.42.0

NEW FEATURES

MINOR CHANGES

BUG FIXES

BioMM

Changes in version 1.1.10

Changes in version 1.1.9

Changes in version 1.1.8

Changes in version 1.1.7

Changes in version 1.1.6

Changes in version 1.1.5

Changes in version 1.1.4

Changes in version 1.1.3

Changes in version 1.1.2

Changes in version 1.1.1

Changes in version 1.1.0

BioQC

Changes in version 1.13.1

biosigner

Changes in version 1.13.20

BUG FIXED

Changes in version 1.13.18

MINOR MODIFICATION

Changes in version 1.13.16

MINOR MODIFICATION

Changes in version 1.13.14

MINOR MODIFICATION

Changes in version 1.13.12

INTERNAL MODIFICATION

Changes in version 1.13.10

INTERNAL MODIFICATION

Changes in version 1.13.8

NEW FEATURE

Changes in version 1.13.6

NEW FEATURES

Changes in version 1.13.4

MINOR MODIFICATION

Changes in version 1.13.2

NEW FEATURE

blacksheepr

Changes in version 0.99.13 (2019-10-11)

Changes in version 0.99.9 (2019-09-30)

Changes in version 0.99.7 (2019-09-10)

breakpointR

Changes in version 1.2.1

brendaDb

Changes in version 0.99.21 (2019-10-17)

Changes in version 0.99.20 (2019-08-16)

Changes in version 0.99.10 (2019-08-12)

Changes in version 0.99.0 (2019-07-22)

BUSpaRse

Changes in version 0.99.25 (2019-09-11)

Changes in version 0.99.24 (2019-09-06)

Changes in version 0.99.23 (2019-09-06)

Changes in version 0.99.20 (2019-08-26)

Changes in version 0.99.19 (2019-07-23)

Changes in version 0.99.0 (2019-06-21)

CAGEfightR

Changes in version 1.5.3

Changes in version 1.5

CAGEr

Changes in version 1.28.0

BACKWARDS-INCOMPATIBLE CHANGES

NEW FEATURES

BUG FIXES

calm

Changes in version 0.99.0 (2019-07-18)

CAMERA

Changes in version 1.41.1

NEW FEATURES

canceR

Changes in version 1.19.05

Changes in version 1.19.04

Changes in version 1.19.03

Changes in version 1.19.02

Changes in version 1.19.01

Cardinal

Changes in version 2.3.18 (2019-10-27)

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 2.3.17 (2019-10-25)

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 2.3.16 (2019-10-14)

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 2.3.15 (2019-10-13)

NEW FEATURES

Changes in version 2.3.14

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 2.3.13

BUG FIXES

Changes in version 2.3.12

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 2.3.11

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 2.3.10

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 2.3.9

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 2.3.8

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 2.3.7

NEW FEATURES

BUG FIXES

Changes in version 2.3.6

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 2.3.5

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 2.3.4

NEW FEATURES

Changes in version 2.3.3

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 2.3.2

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 2.3.1

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 2.2.4

BUG FIXES

Changes in version 2.2.3

BUG FIXES

Changes in version 2.2.2

BUG FIXES

Changes in version 2.2.1

BUG FIXES

cbaf

Changes in version 1.8.0 (2019-10-28)

New Features

ccfindR

Changes in version 1.5.0

Changes

Changes in version 1.4.1

Changes

celda

Changes in version 1.1.6 (2019-07-16)

Changes in version 1.1.4 (2019-05-28)

Changes in version 1.1.3 (2019-05-14)

Changes in version 1.1.2 (2019-05-14)

Changes in version 1.1.1 (2019-05-09)

CellBench

Changes in version 1.1.3

Bug Fixes

Changes in version 1.1.2

Bug Fixes

Modifications

Changes in version 1.1.1

New Features

CellMixS

Changes in version 1.1.3

ChAMP

Changes in version 2.15.1

Chicago

Version: 1.13 Category: Defaults are now updated based on .npb file header rather than just checking them for consistency with it Text:

Version: 1.13 Category: When using Chicago with four-cutter enzymes, make sure you reduce minFragLen parameter. However, this can now only be done when generating the design files, and not in the R package itself Text:

chipenrich

Changes in version 2.10.0

NEW FEATURES

IMPROVEMENTS

BUG FIXES

ChIPpeakAnno

Changes in version 3.19.5

Changes in version 3.19.4

Changes in version 3.19.3

Changes in version 3.19.2

Changes in version 3.19.1

ChIPseeker

Changes in version 1.21.1

chromstaR

Changes in version 1.11.1

BUGFIXES

circRNAprofiler

Changes in version 0.1.1 (2019-05-30)

cleanUpdTSeq

Changes in version 1.23.1

clusterExperiment

Changes in version 2.5.7

Bugs:

Changes in version 2.5.3

Changes

Bugs

CNVRanger

Changes in version 1.2.0

cola

Changes in version 1.1.2

Changes in version 1.1.1

ComplexHeatmap

Changes in version 2.1.1

Changes in version 2.1.0

consensusDE

Changes in version 1.3.4 (2019-09-16)

Changes in version 1.3.3 (2019-06-27)

Changes in version 1.3.2 (2019-06-21)

Changes in version 1.3.1 (2019-06-18)

consensusOV

Changes in version 1.8.0

CRISPRseek

Changes in version 1.25.6

Changes in version 1.25.5

Changes in version 1.25.4

Changes in version 1.25.1

NEW FEATURES

CrossICC

Changes in version 0.99.27 (2019-10-22)

Changes in version 0.99.26 (2019-09-23)

Changes in version 0.99.24 (2019-09-23)

Changes in version 0.99.23 (2019-09-14)

Changes in version 0.99.22 (2019-09-06)

Changes in version 0.99.21 (2019-09-06)

Changes in version 0.99.20 (2019-07-30)

Changes in version 0.99.19 (2019-07-29)

Changes in version 0.99.18 (2019-07-29)

Changes in version 0.99.17 (2019-07-29)

Changes in version 0.99.16 (2019-07-29)

Changes in version 0.99.15 (2019-07-28)

Changes in version 0.99.14 (2019-07-28)

Changes in version 0.99.13 (2019-07-28)

Changes in version 0.99.12 (2019-07-28)

Changes in version 0.99.11 (2019-07-28)

Changes in version 0.99.10 (2019-07-27)

Changes in version 0.99.9 (2019-07-27)

Changes in version 0.99.8 (2019-07-27)

Changes in version 0.99.7 (2019-07-26)

Changes in version 0.99.6 (2019-07-26)

Changes in version 0.99.5 (2019-07-26)

Changes in version 0.99.4 (2019-07-26)

Changes in version 0.99.3 (2019-07-26)

Changes in version 0.99.2 (2019-07-25)

Changes in version 0.99.1 (2019-07-25)

Changes in version 0.1.1 (2019-06-25)

Changes in version 0.1.0 (2019-06-25)

csaw

Changes in version 1.20.0

cTRAP

Changes in version 1.4

New features

Major changes

Bug fixes and minor changes

Changes in version 1.23.5

Changes in version 1.23.4

Changes in version 1.23.3

Changes in version 1.23.1

debCAM

Changes in version 1.3.3 (2019-10-28)

Changes in version 1.1.1 (2018-12-28)

debrowser

Changes in version 1.12.2

deco

Changes in version 1.0.1

decompTumor2Sig

Changes in version 2.1.0 (2019-08-18)

deepSNV

Changes in version 1.99.3 (2013-07-25)

Updates

Bugfixes

Changes in version 1.99.2 (2013-07-11)

Updates

Bugfixes

Changes in version 1.99.1 (2013-06-25)

Updates

Bugfixes

Changes in version 1.99.0 (2013-04-30)

Updates

DEGreport

Changes in version 1.21.1

DelayedArray

Changes in version 0.12.0

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

DepecheR

Changes in version 1.1.9 (2019-10-06)

Changes in version 1.1.8 (2019-09-12)

Changes in version 1.1.6 (2019-09-12)

Changes in version 1.1.5 (2019-08-07)

Changes in version 1.1.4 (2019-07-30)

Changes in version 1.1.3 (2019-06-28)

Changes in version 1.1.2 (2019-06-28)

derfinder

Changes in version 1.19.9

BUG FIXES

Changes in version 1.19.8

Changes in version 1.19.4

BUG FIXES

sampleFile <- c(‘SRR387777’ = ‘http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw’) regs <- GenomicRanges::GRanges(‘chrY’, IRanges(start = c(1, 1), width = 10), strand = ‘-‘) names(regs) <- c(1:2) result <- rtracklayer::import(sampleFile, selection = regs, as = ‘RleList’)

This error affected recount and other reverse dependencies that use derfinder for processing BigWig files.

Changes in version 1.19.2

BUG FIXES

derfinderHelper

Changes in version 1.19.3

derfinderPlot

Changes in version 1.19.3

DESeq2

Changes in version 1.26.0

DEWSeq

Changes in version 0.99.0 (2019-09-23)

DiffBind

Changes in version 3.13.1

diffcyt

Changes in version 1.5.6

DiscoRhythm

Changes in version 1.1.1 (2019-09-27)

DMCFB

Changes in version 0.99.1

New Features

CHANGES IN VERSION 0.99.1 (2019-06-02)

Added

Changed

Removed

Fixed

DMRcate

Changes in version 2.0.0

DominoEffect

Changes in version 1.5.2

UDPATE

Changes in version 1.5.1

UDPATE

Changes in version 1.5.0

UDPATE

DOSE

Changes in version 3.11.2

Changes in version 3.11.1

DropletUtils

Changes in version 1.8.0

Changes in version 1.6.0

edgeR

Changes in version 3.28.0

EnhancedVolcano

Changes in version 1.4

enrichplot

Changes in version 1.5.2

Changes in version 1.5.1

ensemblVEP

Changes in version 1.28.0

epivizrServer

Changes in version 999.999

ExperimentHub

Changes in version 1.11.0

NEW FEATURES

BUG FIXES

FamAgg

Changes in version 1.13.1

fcScan

Changes in version 0.99

FELLA

Changes in version 1.5.3

Changes in version 1.4.2

Changes in version 1.4.1

fgsea

Changes in version 1.11.2

Changes in version 1.11.1

fishpond

Changes in version 1.2.0

flowcatchR

Changes in version 1.20.0

Bug fixes

flowDensity

Changes in version 1.19.8

flowSpecs

Changes in version 0.99.4 (2019-09-30)

Changes in version 0.99.3 (2019-09-18)

Changes in version 0.99.2 (2019-09-18)

Changes in version 0.99.1 (2019-09-18)

Changes in version 0.9.2 (2019-09-17)

Changes in version 0.9.1 (2019-09-16)

flowSpy

Version: 2018-12-19 Text:

Version: 2019-03-31 Text:

Version: 2019-05-04 Text:

Version: 2019-05-07 Text:

Version: 2019-05-29 Text:

Version: 2019-08-08 Text:

FoldGO

Changes in version 1.2.3 (2019-07-17)

Changes in version 1.2.2 (2019-07-16)

Changes in version 1.2.1

GCSscore

Changes in version 1.0.0

GDSArray

Changes in version 1.5.3

NEW FEATURES

BUG FIXES

gdsfmt

Changes in version 1.22.0

NEW FEATURES

UTILITIES

BUG FIXES

gemini

Changes in version 0.3.0

geneClassifiers

Changes in version 1.9.0

GENESIS

Changes in version 2.15.3

GenomicAlignments

Changes in version 1.22.0

NEW FEATURES

BUG FIXES

GenomicFeatures

Changes in version 1.38.0

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

GenomicOZone

Changes in version 0.99.9

Changes in version 0.99.8

Changes in version 0.99.7

Changes in version 0.99.6

Changes in version 0.99.5

Changes in version 0.99.4

Changes in version 0.99.3

Changes in version 0.99.2

Changes in version 0.99.1

Changes in version 0.99.0

GenomicRanges

Changes in version 1.38.0

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

GenomicScores

Changes in version 1.10.0

USER VISIBLE CHANGES

BUG FIXES

ggtree

Changes in version 1.99.1

Changes in version 1.99.0

Changes in version 1.17.5

Changes in version 1.17.4

Changes in version 1.17.3

Changes in version 1.17.2

Changes in version 1.17.1

GNET2

Changes in version 1.1.3

Changes in version 1.1.2

Changes in version 1.1.1

GOfuncR

Changes in version 1.5.2

USER-LEVEL CHANGES

Changes in version 1.5.1

NEW FEATURES

graphite

Changes in version 1.31.1 (2019-10-24)

gscreend

Changes in version 0.99.4

GSEABenchmarkeR

Changes in version 1.6.0

GSVA

Changes in version 1.34

BUG FIXES

gtrellis

Changes in version 1.17.1

Gviz

Changes in version 1.29.1

NEW FEATURES

BUG FIXES

HDF5Array

Changes in version 1.14.0

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

HDTD

Changes in version 1.19.1 (2019-10-24)

hiAnnotator

Changes in version 1.19.0

HIBAG

Changes in version 1.22.0

HiLDA

Changes in version 0.99.11 (2019-09-10)

Changes in version 0.99.10 (2019-07-24)

Changes in version 0.99.9 (2019-07-24)

Changes in version 0.99.8 (2019-06-22)

Changes in version 0.99.7 (2019-06-22)

Changes in version 0.99.6 (2019-06-22)

Changes in version 0.99.5 (2019-06-22)

Changes in version 0.99.4 (2019-06-22)

Changes in version 0.99.3 (2019-06-21)

Changes in version 0.99.2 (2019-06-05)

Changes in version 0.99.1 (2019-06-04)

hipathia

Changes in version 2.1.1 (2019-05-17)

HIREewas

Changes in version 1.3.1

HPAanalyze

Changes in version 1.3

ideal

Changes in version 1.10.0

New features

Bug fixes

Other notes

idr2d

Changes in version 0.99.2

Changes in version 0.99.1

Changes in version 0.99.0

IgGeneUsage

Changes in version 0.99.0 (2019-07-15)

igvR

Changes in version 1.6

NEW FEATURES

immunoClust

Changes in version 1.17.3

Changes in version 1.17.2

Changes in version 1.17.1

infercnv

Changes in version 1.1.4 (2019-10-29)

Changes in version 1.1.3 (2019-09-16)

Changes in version 1.1.2 (2019-07-08)

Changes in version 1.1.1 (2019-05-20)

Changes in version 1.0.4 (2019-09-16)

Changes in version 1.0.3 (2019-07-05)

Changes in version 1.0.2 (2019-05-21)

Changes in version 1.0.1 (2019-05-20)

InPAS

Changes in version 1.17.3

Changes in version 1.17.2

IRanges

Changes in version 2.20.0

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

iSEE

Changes in version 1.5.13

Changes in version 1.5.12

Changes in version 1.5.11

Changes in version 1.5.10

Changes in version 1.5.9

Changes in version 1.5.8

Changes in version 1.5.7

Changes in version 1.5.6

Changes in version 1.5.5

Changes in version 1.5.4

Changes in version 1.5.3

Changes in version 1.5.2

Changes in version 1.5.1

Changes in version 1.5.0

IsoformSwitchAnalyzeR

Changes in version 1.7.2 (2019-10-18)

Changes in version 1.7.1 (2019-07-19)

kebabs

Changes in version 1.20.0

Changes in version 1.19.1

Changes in version 1.19.0

KEGGprofile

Changes in version 1.27.4

Changes in version 1.27.3

Changes in version 1.27.2

Changes in version 1.27.1

KnowSeq

Changes in version 0.99.55 (2019-10-09)

Changes in version 0.99.51 (2019-08-19)

Changes in version 0.99.42

Changes in version 0.99.31 (2019-07-17)

Changes in version 0.99.30 (2019-06-05)

limma

Changes in version 3.42.0

lionessR

Changes in version 0.99.2 (2019-09-30)

Changes in version 0.99.1 (2019-09-05)

Changes in version 0.99.0 (2019-08-19)

lipidr

Changes in version 1.99.2

Maaslin2

Changes in version 0.99.15 (2019-08-05)

Changes in version 0.99.14 (2019-07-31)

Changes in version 0.99.13 (2019-07-31)

Changes in version 0.99.12 (2019-07-26)

Changes in version 0.99.11 (2019-07-24)

Changes in version 0.99.10 (2019-07-19)

Changes in version 0.99.9 (2019-07-18)

Changes in version 0.99.8 (2019-07-18)

Changes in version 0.99.7 (2019-07-17)

Changes in version 0.99.6 (2019-07-17)

Changes in version 0.99.5 (2019-07-17)

Changes in version 0.99.4 (2019-07-17)

Changes in version 0.99.3 (2019-07-17)

Changes in version 0.99.2 (2019-06-27)

Changes in version 0.99.1 (2019-06-05)

Changes in version 0.99.0 (2019-05-24)

Changes in version 0.3.0 (2019-05-20)

Changes in version 0.2.3 (2018-12-20)

Changes in version 0.2.2 (2018-11-15)

Changes in version 0.2.1 (2018-10-10)

Changes in version 0.2.0 (2018-10-09)

Changes in version 0.1.0 (2018-09-27)

MACSQuantifyR

Changes in version 0.99.0 (2018-11-14)

maftools

Changes in version 2.2.0

NEW FUNCTIONS AND FEATURES

DEPRECATED

SIGNIFICANT USER-LEVEL IMPROVEMENT

BUG FIX

MAGeCKFlute

Changes in version 1.4.3

Changes in version 1.4.1

matter

Changes in version 1.11.7 (2019-10-25)

BUG FIXES

Changes in version 1.11.6 (2019-10-23)

NEW FEATURES

Changes in version 1.11.5 (2019-10-13)

NEW FEATURES

Changes in version 1.11.4 (2019-10-13)

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.11.3

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.11.2

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.11.1

NEW FEATURES

MEB

Changes in version 0.99.3

Changes in version 0.99.2

Changes in version 0.99.1

Changes in version 0.99.0

MetaboSignal

Changes in version 1.14.1

metagene2

Changes in version 1.1.4 (2019-07-12)

Changes in version 1.1.3 (2019-05-13)

Changes in version 1.1.2 (2019-05-09)

Changes in version 1.1.1 (2019-05-03)

Changes in version 1.1.0 (2019-04-05)

metaMS

Changes in version 1.21.4

Changes in version 1.21.2

MetCirc

Changes in version 1.15.2 (2019-09-09)

Changes in version 1.15.1 (2019-08-29)

Changes in version 1.15.0 (2019-04-23)

MethCP

Changes in version 0.99.0

methrix

Changes in version 0.99.0

o Submission to Bioconductor

methylGSA

Changes in version 1.3.5

Changes in version 1.3.2

Changes in version 1.3.1

MGFR

Changes in version 1.10.1

microbiome

Changes in version 2.0 (2019-08-20)

microbiomeDASim

Changes in version 0.99.0 (2019-08-26)

miRSM

Changes in version 1.3.2

Changes in version 1.3.1

miRspongeR

Changes in version 1.11.1

mixOmics

Changes in version 6.8.6

new features / enhancements

-

bug fixes

minor improvements

Changes in version 6.8.5

bug fixes

Changes in version 6.8.4

minor improvements

Changes in version 6.8.3

new features / enhancements

bug fixes

minor improvements

Changes in version 6.8.2

minor improvements

Changes in version 6.8.1

bug fixes

minor improvements

MMAPPR2

Changes in version 0.99.0

MMUPHin

Changes in version 0.99.2 (2019-10-21)

Changes in version 0.99.1 (2019-10-15)

Changes in version 0.99.0 (2019-10-15)

MOSim

Changes in version 0.99.0 (2019-06-13)

motifStack

Changes in version 1.29.8

Changes in version 1.29.7

Changes in version 1.29.6

Changes in version 1.29.5

Changes in version 1.29.4

Changes in version 1.29.3

Changes in version 1.29.2

Changes in version 1.29.1

msa

Changes in version 1.18.0

Changes in version 1.17.2

Changes in version 1.17.1

Changes in version 1.17.0

MSnbase

Changes in version 2.11

Changes in 2.11.13

Changes in 2.11.12

Changes in 2.11.11

Changes in 2.11.10

Changes in 2.11.9

Changes in 2.11.8

Changes in 2.11.7

Changes in 2.11.6

Changes in 2.11.5

Changes in 2.11.4

Changes in 2.11.3

Changes in 2.11.2

Changes in 2.11.1

Changes in 2.11.0

msPurity

Changes in version 1.11.5

Changes in version 1.11.3

Changes in version 1.11.2

Changes in version 1.11.1

Changes in version 1.11.0

mzR

Changes in version 2.19.6

Changes in version 2.19.5

Changes in version 2.19.4

Changes in version 2.19.3

Changes in version 2.19.2

Changes in version 2.19.1

NADfinder

Changes in version 1.9.2

Changes in version 1.9.1

NBAMSeq

Changes in version 1.1.1 (2019-08-16)

ncGTW

Changes in version 0.99.7 (2019-08-22)

Changes in version 0.99.2 (2019-06-19)

Changes in version 0.5.0 (2019-04-02)

netboost

Changes in version 1.1.3 (2019-08-01)

Changes in version 1.1.1 (2019-05-06)

ngsReports

Changes in version 1.1.1

Changes in version 1.0.2

Changes in version 1.0.1

NormalyzerDE

Changes in version 1.3.3

Changes in version 1.3.2

Changes in version 1.3.0

normr

Changes in version 1.11.2

Changes in version 1.11.1

omicplotR

Changes in version 1.5.4

Changes in version 1.5.1

OmnipathR

Changes in version 0.99.12 (2019-10-21)

Changes in version 0.99.0 (2019-10-10)

OncoSimulR

Changes in version 2.15.2 (2019-08-14)

Changes in version 2.15.1 (2019-06-06)

Changes in version 2.15.0 (2019-06-06)

onlineFDR

Changes in version 1.4.0

MODIFICATIONS

oppti

Changes in version 0.99.13

Features in the first version, Bioconductor 3.10 Release (September 2019

Organism.dplyr

Changes in version 1.14.0

NEW FEATURES

OUTRIDER

Changes in version 1.3.2

pathwayPCA

Changes in version 1.1.1

2019-06-06

Our build on Bioconductor 3.9 devel fails for the second vignette. This patch resolves this issue.

Pbase

Changes in version 0.25.1

pcaExplorer

Changes in version 2.12.0

Bug fixes

Other notes

PCAtools

Changes in version 2.0.0

peakPantheR

Changes in version 0.99.3 (2019-10-01)

Changes in version 0.99.2 (2019-09-10)

Changes in version 0.99.0 (2019-06-09)

PERFect

Changes in version 0.99.11 (2019-09-19)

Changes in version 0.99.10 (2019-09-17)

PGA

Changes in version 1.15.1

Changes in version 1.14.1

PhyloProfile

Changes in version 0.99.31

piano

Changes in version 2.2.0

BUG FIXES

Changes in version 2.0.1

BUG FIXES

Pigengene

Changes in version 1.11.34 (2019-10-21)

General

Changes in version 1.11.32 (2019-10-18)

Changes in existing functions

Changes in version 1.11.30 (2019-10-02)

Changes in existing functions

Changes in version 1.11.28 (2019-10-01)

New functions

Changes in version 1.11.26 (2019-09-26)

Changes in existing functions

New functions

Changes in version 1.11.24 (2019-09-03)

Bug Fixes

Changes in version 1.11.20 (2019-05-15)

Changes in existing functions

Changes in version 1.11.4 (2019-05-02)

Bug Fixes

podkat

Changes in version 1.18.0

Changes in version 1.17.3

Changes in version 1.17.2

Changes in version 1.17.1

Changes in version 1.17.0

polyester

Changes in version 1.99.3

Changes in version 1.99.2

pqsfinder

Changes in version 2.2

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

proDA

Changes in version 0.99.0 (2019-06-02)

pRoloc

Changes in version 1.25

Changes in version 1.25.2

Changes in version 1.25.1

Changes in version 1.25.0

ProtGenerics

Changes in version 1.17.4

Changes in version 1.17.3

Changes in version 1.17.2

Changes in version 1.17.1

PureCN

Changes in version 1.16.0

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUGFIXES

pwrEWAS

Changes in version 0.1.0

QDNAseq

Changes in version 1.21.6 (2019-09-25)

BUG FIXES

Changes in version 1.21.5 (2019-09-09)

BUG FIXES

Changes in version 1.21.4 (2019-09-06)

SIGNIFICANT CHANGES

Changes in version 1.21.3 (2019-09-04)

NEW FEATURES

IMPROVEMENTS

DEPRECATION AND DEFUNCT

Changes in version 1.21.2 (2019-09-03)

SIGNIFICANT CHANGES

IMPROVEMENTS

SOFTWARE QUALITY

Changes in version 1.21.1 (2019-08-30)

SIGNIFICANT CHANGES

qPLEXanalyzer

Changes in version 1.3.2

Changes in version 1.3.1

Qtlizer

Changes in version 0.99.12 (2019-09-06)

Changes in version 0.99.11 (2019-09-03)

Changes in version 0.99.10 (2019-08-27)

Changes in version 0.99.9 (2019-08-27)

Changes in version 0.99.8 (2019-08-27)

Changes in version 0.99.7 (2019-08-27)

Changes in version 0.99.6 (2019-08-27)

Changes in version 0.99.5 (2019-08-27)

Changes in version 0.99.4 (2019-08-14)

Changes in version 0.99.0 (2019-08-12)

RaggedExperiment

Changes in version 1.10.0

Bug fixes and minor improvements

Rcpi

Changes in version 1.21.1 (2019-05-17)

Improvements

Rcwl

Changes in version 1.1.12 (2019-09-09)

Changes in version 1.1.7 (2019-07-25)

RcwlPipelines

Changes in version 1.1.14 (2019-10-21)

Changes in version 1.1.8 (2019-08-22)

Changes in version 1.1.5 (2019-07-19)

Changes in version 1.1.2 (2019-05-22)

RCy3

Changes in version 2.6.0

Changes in version 2.4.4

Changes in version 2.4.3

Changes in version 2.4.2

Changes in version 2.4.1

ReactomeGSA

Changes in version 0.99.8 (2019-08-13)

Changes in version 0.99.7 (2019-07-22)

Changes in version 0.99.6 (2019-07-09)

Changes in version 0.99.5 (2019-07-09)

Changes in version 0.99.0 (2019-07-01)

recount

Changes in version 1.11.14

Changes in version 1.11.13

NEW FEATURES

Changes in version 1.11.12

BUG FIXES

Changes in version 1.11.7

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.11.4

NEW FEATURES

regioneR

Changes in version 1.18.0

NEW FEATURES

BUG FIXES

regionReport

Changes in version 1.19.2

SIGNIFICANT USER-VISIBLE CHANGES

rGREAT

Changes in version 1.17.1

rhdf5

Changes in version 2.30.0

NEW FEATURES

BUG FIXES

Rhdf5lib

Changes in version 1.8

New features

Bug fixes

Rhtslib

Changes in version 1.18.0

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

RNAmodR

Changes in version 0.99.0 (2019-04-29)

RNAmodR.AlkAnilineSeq

Changes in version 0.99.0 (2019-04-29)

RNAmodR.ML

Changes in version 0.99.0 (2019-04-29)

RNAmodR.RiboMethSeq

Changes in version 0.99.0 (2019-04-29)

RnBeads

Changes in version 2.3.3

Changes in version 2.3.2

rols

Changes in version 2.13

CHANGES IN VERSION 2.13.2

CHANGES IN VERSION 2.13.1

ropls

Changes in version 1.17.34

NEW FEATURE

Changes in version 1.17.32

BUG FIXED

Changes in version 1.17.30

MINOR MODIFICATION

Changes in version 1.17.28

MINOR MODIFICATION

Changes in version 1.17.26

MINOR MODIFICATION

Changes in version 1.17.24

MINOR MODIFICATION

Changes in version 1.17.22

INTERNAL MODIFICATION

Changes in version 1.17.20

NEW FEATURE

Changes in version 1.17.18

INTERNAL MODIFICATION

Changes in version 1.17.16

INTERNAL MODIFICATION

Changes in version 1.17.14

NEW FEATURE

Changes in version 1.17.12

NEW FEATURE

Changes in version 1.17.10

NEW FEATURE

Changes in version 1.17.8

NEW FEATURE

Changes in version 1.17.6

INTERNAL MODIFICATION

Changes in version 1.17.4

INTERNAL MODIFICATION

Changes in version 1.17.2

NEW FEATURE

rpx

Changes in version 1.21

Changes in version 1.21.3

Changes in version 1.21.2

Changes in version 1.21.1

Rsubread

Changes in version 2.0.0

RTCA

Changes in version 2009-07-13

RTCGAToolbox

Changes in version 2.16.0

New features

Bug fixes and minor improvements

rWikiPathways

Changes in version 1.6.0

Changes in version 1.4.1

S4Vectors

Changes in version 0.24.0

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

SAIGEgds

Changes in version 1.0.0

Changes in version 0.99.0

Changes in version 0.9.10

Changes in version 0.9.9

Changes in version 0.9.7

Changes in version 0.9.0

scater

Changes in version 1.14.0

scds

Changes in version 1.2.0

schex

Changes in version 0.99.7

Changes in version 0.99.6

Changes in version 0.99.5

Changes in version 0.99.4

Changes in version 0.99.3

scMerge

Changes in version 1.1.6

Changes in version 1.1.5

Changes in version 1.1.4

Changes in version 1.1.3

Changes in version 1.1.2

Changes in version 1.1.0

scPCA

Changes in version 0.99.0 (2019-09-13)

scran

Changes in version 1.14.0

scTensor

Changes in version 1.2.0

scTGIF

Changes in version 0.99.0

SeqArray

Changes in version 1.26.0

NEW FEATURES

UTILITIES

BUG FIXES

CHANGES

Changes in version 1.24.2

NEW FEATURES

UTILITIES

BUG FIXES

seqCAT

Changes in version 1.8.0

Features

sevenbridges

Changes in version 1.15.1

Improvements

SharedObject

Changes in version 0.99.2

Changes in version 0.99.0 (2019-05-16)

signatureSearch

Changes in version 1.1.0 (2019-10-23)

Changes in version 0.99.20 (2019-10-22)

signeR

Changes in version 1.11.1

SIMLR

Changes in version 1.11.1 (2019-10-13)

SingleCellExperiment

Changes in version 1.8.0

singscore

Changes in version 1.5.1

sitePath

Changes in version 1.1.10

Changes in version 1.1.9

Changes in version 1.1.8

Changes in version 1.1.7

Changes in version 1.1.6

Changes in version 1.1.5

Changes in version 1.1.4

Changes in version 1.1.3

Changes in version 1.1.2

Changes in version 1.1.1

SNPRelate

Changes in version 1.20.0

Changes in version 1.18.1

sojourner

Changes in version 0.99.8

Changes in version 0.99.7

Changes in version 0.99.6

Changes in version 0.99.5

Changes in version 0.99.4

Changes in version 0.99.3

Changes in version 0.99.2

Changes in version 0.99.1

Changes in version 0.99.0

Spaniel

Changes in version 0.99.0

SpatialCPie

Changes in version 1.1

splatter

Changes in version 1.10.0 (2019-10-20)

SQLDataFrame

Changes in version 1.0.0 (2019-10-01)

NEW FEATURES

BUG FIXES

Changes in version 0.99.0 (2019-04-05)

sRACIPE

Changes in version 1.1.3 (2019-10-17)

Changes in version 1.1.2 (2019-10-17)

ssrch

Changes in version 1.1.1

statTarget

Changes in version 2.0

NEW FEATURES

Changes in version 1.15.4

Changes in version 1.15.3

Structstrings

Changes in version 1.1.6 (2019-09-23)

SummarizedBenchmark

Changes in version 2.3.7 (2019-09-18)

Changes in version 2.3.6 (2019-09-06)

Changes in version 2.3.5 (2019-06-22)

Changes in version 2.3.4 (2019-06-18)

Changes in version 2.3.3 (2019-06-14)

SummarizedExperiment

Changes in version 1.16.0

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

SynMut

Changes in version 1.1.3 (2019-05-08)

Changes in version 1.1.2 (2019-05-08)

Changes in version 1.1.1 (2019-05-06)

Changes in version 1.1.0 (2019-05-06)

target

Changes in version 0.1.0

TargetSearch

Changes in version 1.42.0

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

BUG FIXES

TCGAutils

Changes in version 1.6.0

New features

Minor changes and bug fixes

TOAST

Changes in version 0.99.7

Changes in version 0.99

NEW FEATURES

tofsims

Changes in version 099.1

SIGNIFICANT USER-VISIBLE CHANGES

INTERNALS

topconfects

Changes in version 1.1.4 (2018-12-29)

Changes in version 1.1.3 (2018-11-14)

Changes in version 1.1.2 (2018-06-30)

Changes in version 1.1.1 (2019-09-20)

Changes in version 1.0.1 (2018-02-04)

topdownr

Changes in version 1.7

Changes in version 1.7.1

Changes in version 1.7.2

TPP

Changes in version 3.13.3

Changes in version 3.13.2

Changes in version 3.13.1

TPP2D

Changes in version 1.1.0 (2019-05-06)

trackViewer

Changes in version 1.21.18

Changes in version 1.21.17

Changes in version 1.21.16

Changes in version 1.21.15

Changes in version 1.21.14

Changes in version 1.21.13

Changes in version 1.21.12

Changes in version 1.21.11

Changes in version 1.21.10

Changes in version 1.21.9

Changes in version 1.21.8

Changes in version 1.21.7

Changes in version 1.21.6

Changes in version 1.21.5

Changes in version 1.21.4

Changes in version 1.21.3

Changes in version 1.21.2

Changes in version 1.21.1

tradeSeq

Changes in version 0.99.9902 (2019-10-23)

Changes in version 0.99.47 (2019-09-02)

Changes in version 0.99.0 (2019-06-22)

Changes in version 0.9.0 (2019-03-15)

transite

Changes in version 1.2.1

treeio

Changes in version 1.9.3

Changes in version 1.9.2

Changes in version 1.9.1

tRNAscanImport

Changes in version 1.5.3 (2019-08-25)

TSRchitect

Changes in version 1.11.12

tximeta

Changes in version 1.4.0

tximport

Changes in version 1.14.0

Ularcirc

Changes in version 1.3.22

NEW FEATURES

BUG FIXES

Changes in version 1.3.1

BUG FIXES

universalmotif

Changes in version 1.4.0

NEW FEATURES

MINOR CHANGES

BUG FIXES

Changes in version 1.2.1

BUG FIXES

variancePartition

Changes in version 1.15.8

Changes in version 1.15.7

Changes in version 1.15.6

Changes in version 1.15.4

Changes in version 1.15.3

Changes in version 1.15.2

Changes in version 1.15.0

VariantExperiment

Changes in version 0.99.8

ViSEAGO

Changes in version 0.99.42

Changes in version 0.99.41

Changes in version 0.99.40

Changes in version 0.99.39

Changes in version 0.99.38

Changes in version 0.99.37

Changes in version 0.99.36

Changes in version 0.99.35

Changes in version 0.99.34

Changes in version 0.99.33

Changes in version 0.99.32

Changes in version 0.99.30

waddR

Changes in version 0.99.6 (2019-10-28)

Changes in version 0.99.5 (2019-10-14)

Changes in version 0.99.4 (2019-10-01)

Changes in version 0.99.3 (2019-08-30)

Changes in version 0.99.2 (2019-08-27)

Changes in version 0.99.0 (2019-08-27)

Changes in version 0.2.8 (2019-08-19)

Changes in version 0.2.7 (2019-08-13)

Changes in version 0.2.6 (2019-08-08)

Changes in version 0.2.5 (2019-08-06)

Changes in version 0.2.4 (2019-07-31)

Changes in version 0.2.3 (2019-07-29)

Changes in version 0.2.2 (2019-07-29)

xcms

Changes in version 3.7.5

Changes in version 3.7.4

Changes in version 3.7.3

Changes in version 3.7.2

Changes in version 3.7.1

zinbwave

Changes in version 1.7.5 (2019-10-08)

NEWS from new and existing Data Experiment Packages

benchmarkfdrData2019

Changes in version 0.99.15 (2019-06-06)

Changes in version 0.99.14 (2019-05-08)

Changes in version 0.99.13 (2019-05-08)

Changes in version 0.99.12 (2019-05-07)

Changes in version 0.99.11 (2019-05-06)

Changes in version 0.99.10 (2019-05-06)

Changes in version 0.99.9 (2019-05-06)

Changes in version 0.99.8 (2019-05-04)

Changes in version 0.99.7 (2019-04-24)

Changes in version 0.99.6 (2019-04-24)

Changes in version 0.99.5 (2019-04-23)

Changes in version 0.99.4 (2019-04-23)

Changes in version 0.99.3 (2019-04-23)

Changes in version 0.99.2 (2019-04-23)

Changes in version 0.99.1 (2019-04-23)

Changes in version 0.99.0 (2019-04-09)

chipenrich.data

Changes in version 2.10.0

depmap

Changes in version 0.99.6

Changes in version 0.99.0

derfinderData

Changes in version 2.3.4

DMRcatedata

Changes in version 2.0.0

dsQTL

Changes in version 2.17

USER VISIBLE CHANGES

HDCytoData

Changes in version 1.5.4

MMAPPR2data

Changes in version 0.99.20 (2019-05-30)

MouseGastrulationData

Changes in version 0.99.0 (2019-06-17)

PhyloProfileData

Changes in version 0.99.0 (2019-05-30)

PtH2O2lipids

Changes in version 2016-04-21

pwrEWAS.data

Changes in version 0.1.0

RforProteomics

Changes in version 1.23.1

RNAmodR.Data

Changes in version 0.99.0 (2019-04-29)

SBGNview.data

Changes in version 0.99.10

scRNAseq

Changes in version 2.0.0

signatureSearchData

Changes in version 1.1.0 (2019-10-23)

Changes in version 0.99.10 (2019-10-22)

Changes in version 0.99.0 (2019-04-02)

TENxBUSData

Changes in version 0.99.0 (2019-01-08)

NEWS from new and existing Workflows

BgeeCall

Changes in version 1.1.1

Changes in version 1.1.0

CAGEWorkflow

Changes in version 1.1.5

Deprecated and Defunct Packages

Twelve software packages were removed from this release (after being deprecated in Bioc 3.9): flowQ, rMAT, TSSi, flowQB, rSFFreader, ProCoNA, spliceSites, DOQTL, NGScopy, SVM2CRM, miRsponge, htSeqTools

Nineteen software are deprecated in this release and will be removed in Bioc 3.11: SNPchip, rHVDM, GenomeGraphs, plateCore, charm, HTSanalyzeR, PathNet, Rchemcpp, exomePeak, flipflop, Pbase, RnaSeqSampleSize, birte, SEPA, CNPBayes, dSimer, mlm4omics, condcomp, brainImageR

Two experimental data packages were removed in this release (after being deprecated in BioC 3.9): PGPC, flowQBData.

Three experimental data packages are deprecated in this release and will be removed in Bioc 3.11: charmData, facopy.annot, allenpvc.

Two annotation packages were removed this release: MafDb.gnomADex.r2.0.1.GRCh38, MafDb.gnomAD.r2.0.1.GRCh38 (they have been replaced with MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomAD.r2.1.GRCh38)

Two annotation packages are deprecated in this release and will be removed in Bioc 3.11: MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38