Oct 31, 2018

Bioconductors:

We are pleased to announce Bioconductor 3.8, consisting of 1649 software packages, 360 experiment data packages, 941 annotation packages, and 23 workflows.

There are 95 new software packages, 21 new data experiment packages, 2 new workflows, and many updates and improvements to existing packages; Bioconductor 3.8 is compatible with R 3.5.0, 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.

Visit https://bioconductor.org for details and downloads.

Contents

Getting Started with Bioconductor 3.8

To update to or install Bioconductor 3.8:

  1. Install R >=3.5.0. Bioconductor 3.8 has been designed expressly for this version of R.

  2. Follow the instructions at http://bioconductor.org/install/.

New Software Packages

There are 95 new software packages in this release of Bioconductor.

New Data Experiment Packages

There are 21 new data experiment packages in this release of Bioconductor.

New Workflows

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

NEWS from new and existing Software Packages

ABAEnrichment

Changes in version 1.11.7:

USER-LEVEL CHANGES

Changes in version 1.11.6:

USER-LEVEL CHANGES

Changes in version 1.11.3:

Changes in version 1.11.2:

USER-LEVEL CHANGES

Changes in version 1.11.1:

NEW FEATURES

abseqR

Changes in version 0.99.0:

ABSSeq

Changes in version 1.35.2 (2018-06-28):

ACE

Changes in version 0.99.8 (2018-09-06):

Changes in version 0.99.6 (2018-07-26):

Changes in version 0.99.4 (2018-06-26):

IMPROVEMENTS

Changes in version 0.99.0 (2018-05-24):

SUBMISSION

ADaCGH2

Changes in version 2.21.1 (2018-07-16):

affxparser

Changes in version 1.53.2 (2018-10-22):

DOCUMENTATION

Changes in version 1.53.1 (2018-08-28):

Changes in version 1.53.0 (2018-04-30):

AnnotationFilter

Changes in version 1.5.2:

USER VISIBLE CHANGES

AnnotationHubData

Changes in version 1.11.0:

MODIFICATIONS

NEW FEATURES

BUG FIX

anota2seq

Changes in version 1.3.1:

apeglm

Changes in version 1.3.2:

aroma.light

Changes in version 3.11.2 (2018-09-04):

CODE REFACTORING

Changes in version 3.11.1 (2017-08-28):

Changes in version 3.11.0 (2017-04-30):

artMS

Changes in version 0.99.25:

Changes in version 0.99.02:

Changes in version 0.99.01:

ASICS

Changes in version 1.1.1:

Improvements

ASSIGN

Changes in version 1.17.2:

attract

Changes in version 1.33.2 (2018-06-29):

Changes in version 1.33.1 (2018-05-15):

BASiCS

Changes in version 1.3.24 (2018-10-21):

Changes in version 1.3.23 (2018-10-18):

Changes in version 1.3.22 (2018-10-19):

Changes in version 1.3.21 (2018-10-19):

Changes in version 1.3.20 (2018-10-18):

Changes in version 1.3.19 (2018-10-18):

Changes in version 1.3.18 (2018-10-15):

Changes in version 1.3.17 (2018-10-11):

Changes in version 1.3.16 (2018-10-08):

Changes in version 1.3.15 (2018-10-07):

Changes in version 1.3.13 (2018-09-30):

Changes in version 1.3.11 (2018-09-30):

Changes in version 1.3.10 (2018-09-28):

Changes in version 1.3.9 (2018-09-27):

Changes in version 1.3.8 (2018-09-05):

Changes in version 1.3.7 (2018-09-05):

Changes in version 1.3.6 (2018-09-04):

Changes in version 1.3.5 (2018-08-31):

Changes in version 1.3.3 (2018-05-21):

Changes in version 1.3.2 (2018-05-21):

Changes in version 1.3.1 (2018-05-21):

bayNorm

Changes in version 0.99.19:

Changes in version 0.99.9:

Changes in version 0.99.8:

Changes in version 0.99.4:

Changes in version 0.99.1:

Changes in version 0.99.0:

bcSeq

Changes in version 1.3.3:

Changes in version 1.3.2:

Changes in version 1.3.1:

beachmat

Changes in version 1.4.0:

BEclear

Changes in version 1.13.11 (2018-10-25):

Changes in version 1.13.10 (2018-10-24):

Changes in version 1.13.9 (2018-10-23):

Changes in version 1.13.8 (2018-10-22):

Changes in version 1.13.7 (2018-10-10):

Changes in version 1.13.6 (2018-10-05):

Changes in version 1.13.5 (2018-10-04):

Changes in version 1.13.4 (2018-10-02):

Changes in version 1.13.3 (2018-09-28):

Changes in version 1.13.2 (2018-09-27):

Changes in version 1.13.1 (2018-09-25):

BgeeDB

Changes in version 2.6.2:

Changes in version 2.6.1:

BiFET

Changes in version 1.1.5 (2018-07-02):

bioCancer

Changes in version 1.9.07:

Changes in version 1.9.06:

Changes in version 1.9.05:

Changes in version 1.9.04:

Changes in version 1.9.03:

Changes in version 1.9.02:

Changes in version 1.9.01:

BiocCheck

Changes in version 1.17:

NEW FEATURES

BUG FIXES

BiocFileCache

Changes in version 1.5:

NEW FEATURES

BUG FIX

USER-VISIBLE CHANGES

BiocInstaller

Changes in version 1.31.2:

NEW FEATURES

BUG FIXES

BiocNeighbors

Changes in version 1.0.0:

BioCor

Changes in version 1.5.4:

BiocParallel

Changes in version 1.16:

NEW FEATURES

BUG FIXES

breakpointR

Changes in version 0.99.0:

bsseq

Changes in version 1.17:

BUScorrect

Changes in version 0.99.13 (2018-10-09):

Changes in version 0.99.6 (2018-07-27):

CAGEfightR

Changes in version 1.5:

CAGEr

Changes in version 1.24.0:

NEW FEATURES

BUG FIXES

Cardinal

Changes in version 1.99.2 (2018-10-28):

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.99.1 (2018-10-26):

NEW FEATURES

Changes in version 1.99.0 (2018-10-25):

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.13.3 (2018-10-24):

NEW FEATURES

Changes in version 1.13.2:

NEW FEATURES

Changes in version 1.13.1:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.12.1:

BUG FIXES

cbaf

Changes in version 1.4.0 (2018-10-30):

New Features

ccfindR

Changes in version 1.1.2:

Changes

celaref

Changes in version 0.99.1:

BUG FIXES

Changes in version 0.99.0:

NEW FEATURES

CellTrails

Changes in version 0.99.15:

Changes in version 0.99.14:

Changes in version 0.99.13:

Changes in version 0.99.0:

chimeraviz

Changes in version 1.7.1:

CHANGES

ChIPpeakAnno

Changes in version 3.15.2:

Changes in version 3.15.1:

chromstaR

Changes in version 1.7.2:

BUGFIXES

CHRONOS

Changes in version 1.9.2:

Changes in version 1.9.1:

ClassifyR

Changes in version 2.2.0:

clusterExperiment

Changes in version 2.1.5 (2018-06-28):

Changes

Bugs

Changes in version 2.1.4 (2018-06-27):

Bugs

Changes in version 2.1.3 (2018-05-24):

Bugs

Changes in version 2.1.2 (2018-05-17):

Bugs

Changes in version 2.1.1 (2018-05-15):

Bugs:

cogena

Changes in version 1.15.1 (2018-05-30):

COMPASS

Changes in version 1.19.4:

compcodeR

Changes in version 1.17.1:

compEpiTools

Changes in version 1.15.1:

ComplexHeatmap

Changes in version 1.19.1:

consensus

Changes in version 0.99.0:

coRdon

Changes in version 0.99.11:

countsimQC

Changes in version 0.99.0:

Changes in version 0.5.2:

Changes in version 0.5.0:

Changes in version 0.4.6:

Changes in version 0.4.5:

Changes in version 0.4.4:

Changes in version 0.4.2:

Changes in version 0.4.1:

Changes in version 0.4.0:

Changes in version 0.3.2:

Changes in version 0.3.0:

CrispRVariants

Changes in version 1.9.2:

csaw

Changes in version 1.16.0:

customProDB

Changes in version 1.20.3:

UPDATED FUNCTIONS

cydar

Changes in version 1.6.0:

cytofkit

Changes in version 3.6:

dada2

Changes in version 1.9.2:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.9.1:

BUG FIXES

DaMiRseq

Changes in version 1.5.2:

Changes in version 1.4.1:

DChIPRep

Changes in version 1.11.1:

debrowser

Changes in version 1.9.21:

Changes in version 1.8.6:

Changes in version 1.8.4:

Changes in version 1.8.3:

Changes in version 1.8.2:

Changes in version 1.8.1:

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 1.17.8:

Changes in version 1.17.7:

Changes in version 1.17.6:

Changes in version 1.17.5:

Changes in version 1.17.4:

Changes in version 1.17.3:

Changes in version 1.17.1:

DEGseq

Changes in version 1.34.1:

DelayedArray

Changes in version 0.8.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

derfinder

Changes in version 1.15.4:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.15.2:

BUG FIXES

Changes in version 1.15.1:

SIGNIFICANT USER-VISIBLE CHANGES

derfinderHelper

Changes in version 1.15.1:

SIGNIFICANT USER-VISIBLE CHANGES

derfinderPlot

Changes in version 1.15.1:

SIGNIFICANT USER-VISIBLE CHANGES

DESeq2

Changes in version 1.22.0:

Changes in version 1.21.21:

Changes in version 1.21.15:

Changes in version 1.21.14:

Changes in version 1.21.13:

Changes in version 1.21.9:

DEsingle

Changes in version 1.0.5:

Changes in version 1.0.1:

DEsubs

Changes in version 1.7.4:

Changes in version 1.7.3:

Changes in version 1.7.2:

diffHic

Changes in version 1.14.0:

diffuStats

Changes in version 1.0.0:

Director

Changes in version 1.7.3:

DMCHMM

Changes in version 1.3.1:

CHANGES SINCE LAST TIME

dmrseq

Changes in version 1.1.20 (2018-10-11):

Changes in version 1.1.2 (2018-05-09):

DominoEffect

Changes in version 1.1.2:

BUG FIX

Changes in version 1.1.1:

UDPATE

Changes in version 1.1.0:

NEW FEATURES

drawProteins

Changes in version 1.1.1:

FEATURES

DropletUtils

Changes in version 1.2.0:

dupRadar

Changes in version 1.11.1:

edgeR

Changes in version 3.24.0:

EGSEA

Changes in version 1.9.1:

EnhancedVolcano

Changes in version 1.0.0:

EnrichedHeatmap

Changes in version 1.11.1:

EnrichmentBrowser

Changes in version 2.12.0:

ensembldb

Changes in version 2.5.9:

Changes in version 2.5.8:

Changes in version 2.5.6:

Changes in version 2.5.5:

Changes in version 2.5.2:

Changes in version 2.5.1:

ensemblVEP

Changes in version 1.24.0:

NEW FEATURES

ERSSA

Changes in version 0.99.8:

Changes in version 0.99.7:

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 0.99.0:

esetVis

Changes in version 1.7.3:

Changes in version 1.7.2:

Changes in version 1.7.1:

EventPointer

Changes in version 2.0:

ExCluster

Changes in version 0.99.13:

Changes in version 0.99.12:

Changes in version 0.99.11:

Changes in version 0.99.10:

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:

ExperimentHubData

Changes in version 1.7.0:

NEW FEATURES

MODIFICATIONS

FELLA

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:

FGNet

Changes in version 3.15:

fgsea

Changes in version 1.7.1:

flowAI

Changes in version 1.10.1:

flowCL

Changes in version 1.19.1:

Changes in version 1.19.0:

FoldGO

Changes in version 0.99.10 (2018-09-27):

Changes in version 0.99.9:

Changes in version 0.99.8:

Changes in version 0.99.7 (2018-07-19):

Changes in version 0.99.6 (2018-07-19):

Changes in version 0.99.5 (2018-07-16):

Changes in version 0.99.4 (2018-07-16):

Changes in version 0.99.3 (2018-07-13):

Changes in version 0.99.2 (2018-07-12):

Changes in version 0.99.1 (2018-07-12):

Changes in version 0.99.0 (2018-07-12):

gdsfmt

Changes in version 1.17.1-1.17.6:

NEW FEATURES

UTILITIES

BUG FIXES

GeneAccord

Changes in version 0.99.13 (2018-08-02):

genefilter

Changes in version 1.64.0:

NEW FEATURES

GeneNetworkBuilder

Changes in version 1.23.2:

GENESIS

Changes in version 2.12.0:

Changes in version 2.11.15:

Changes in version 2.11.14:

Changes in version 2.11.11:

Changes in version 2.11.8:

Changes in version 2.11.4:

GenomeInfoDb

Changes in version 1.18.0

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

GenomicDataCommons

Changes in version 1.5.8:

GenomicFeatures

Changes in version 1.34.0:

NEW FEATURES

GenomicFiles

Changes in version 1.18.0:

NEW FEATURES

GenomicRanges

Changes in version 1.34.0:

NEW FEATURES

DEPRECATED AND DEFUNCT

BUG FIXES

GenomicScores

Changes in version 1.6.0:

USER VISIBLE CHANGES

genphen

Changes in version 1.9 (2018-10-20):

Changes

To do

GGBase

Changes in version 3.43.1:

GlobalAncova

Changes in version 4.0.0:

GOfuncR

Changes in version 1.1.5:

USER-LEVEL CHANGES

Changes in version 1.1.2:

NEW FEATURES

USER-LEVEL CHANGES

gpart

Changes in version 1.0.0:

NEW FEATURES

graphite

Changes in version 1.27.6 (2018-10-25):

Changes in version 1.27.2 (2018-05-22):

gtrellis

Changes in version 1.13.2:

GWASTools

Changes in version 1.27.1:

HDF5Array

Changes in version 1.10.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

HIBAG

Changes in version 1.17.1:

HilbertCurve

Changes in version 1.11.1:

hipathia

Changes in version 1.1.2 (2018-09-07):

Changes in version 1.0.1 (2018-06-14):

HPAanalyze

Changes in version 0.99.19:

Changes in version 0.99.18:

Changes in version 0.99.17:

Changes in version 0.99.16:

Changes in version 0.99.14:

Changes in version 0.99.13:

Changes in version 0.99.12:

Changes in version 0.99.11:

Changes in version 0.99.10:

hpar

Changes in version 1.23.3:

Changes in version 1.23.2:

Changes in version 1.23.1:

iasva

Changes in version 0.99.3:

MODIFICATIONS

illuminaio

Changes in version 0.23.2 (2018-07-18):

NEW FEATURES

Changes in version 0.23.1 (2018-07-18):

SOFTWARE QUALITY

Changes in version 0.23.0 (2018-05-01):

NOTES

immunoClust

Changes in version 1.13.3:

NEW FEATRUES

CHANGES

InteractionSet

Changes in version 1.10.0:

IntEREst

Changes in version 1.5.2:

NEW FEATURES

BUG FIXES

IPO

Changes in version 1.7.5:

Changes in version 1.7.4:

Changes in version 1.7.3:

Changes in version 1.7.2:

Changes in version 1.7.1:

Changes in version 1.7.0:

Changes in version 1.6.2:

Changes in version 1.6.1:

IRanges

Changes in version 2.16.0

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

iSEE

Changes in version 1.1.13:

Changes in version 1.1.12:

Changes in version 1.1.11:

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 1.0.1:

IsoCorrectoR

Changes in version 0.1.27:

IsoformSwitchAnalyzeR

Changes in version 1.3.10:

Changes in version 1.3.9:

Changes in version 1.3.8:

Changes in version 1.3.7:

Changes in version 1.3.5:

isomiRs

Changes in version 1.9.5:

FIX

Changes in version 1.9.4:

Changes in version 1.9.3:

Changes in version 1.9.2:

Changes in version 1.9.1:

MAJOR

kmknn

Changes in version 1.0.0:

limma

Changes in version 3.38.0:

LRBaseDbi

Changes in version 0.99.17:

Changes in version 0.99.16:

Changes in version 0.99.15:

Changes in version 0.99.14:

Changes in version 0.99.13:

Changes in version 0.99.12:

Changes in version 0.99.11:

Changes in version 0.99.10:

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:

maftools

Changes in version 1.8.0:

NEW FUNCTIONS

SIGNIFICANT USER-LEVEL IMPROVEMENT

MAGeCKFlute

Changes in version 1.1.9:

Changes in version 1.1.6:

Changes in version 1.1.1:

matter

Changes in version 1.7.6:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.7.5:

NEW FEATURES

Changes in version 1.7.4:

NEW FEATURES

Changes in version 1.7.3:

NEW FEATURES

Changes in version 1.7.2:

NEW FEATURES

BUG FIXES

Changes in version 1.7.1:

BUG FIXES

meshes

Changes in version 1.7.1:

MetCirc

Changes in version 1.11.3 (2018-10-22):

Changes in version 1.11.2 (2018-10-15):

methInheritSim

Changes in version 1.3.1:

SIGNIFICANT USER-VISIBLE CHANGES

methylInheritance

Changes in version 1.5.1:

SIGNIFICANT USER-VISIBLE CHANGES

methylKit

Changes in version 1.7.10:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.7.9:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.7.8:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.7.7:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.7.6:

NEW FUNCTIONS AND FEATURES

Changes in version 1.7.4:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.7.3:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.7.2:

NEW FUNCTIONS AND FEATURES

IMPROVEMENTS AND BUG FIXES

MetNet

Changes in version 0.99.24 (2018-10-22):

Changes in version 0.99.23 (2018-10-16):

Changes in version 0.99.20 (2018-08-06):

Changes in version 0.99.19 (2018-07-26):

Changes in version 0.99.18 (2018-07-19):

Changes in version 0.99.17 (2018-07-19):

Changes in version 0.99.15 (2018-07-16):

Changes in version 0.99.14 (2018-07-14):

Changes in version 0.99.13 (2018-07-12):

Changes in version 0.99.12 (2018-07-12):

Changes in version 0.99.11 (2018-07-03):

Changes in version 0.99.10 (2018-07-03):

Changes in version 0.99.9 (2018-06-26):

Changes in version 0.99.8 (2018-06-26):

Changes in version 0.99.6 (2018-06-13):

Changes in version 0.99.5 (2018-06-12):

Changes in version 0.99.4 (2018-06-12):

Changes in version 0.99.3 (2018-06-11):

Changes in version 0.99.2 (2018-06-11):

Changes in version 0.99.1 (2018-06-11):

Changes in version 0.99.0 (2018-05-14):

minfi

Changes in version 1.27:

miRSM

Changes in version 0.99.28:

Changes in version 0.99.27:

Changes in version 0.99.26:

Changes in version 0.99.25:

Changes in version 0.99.24:

Changes in version 0.99.23:

Changes in version 0.99.15-0.99.22:

Changes in version 0.99.8-0.99.14:

Changes in version 0.99.4-0.99.7:

Changes in version 0.99.3:

Changes in version 0.99.2:

Changes in version 0.99.1:

Changes in version 0.99.0:

miRsponge

Changes in version 1.7.5:

Changes in version 1.7.4:

Changes in version 1.7.3:

Changes in version 1.7.2:

Changes in version 1.7.1:

Changes in version 1.7.0:

missMethyl

Changes in version 1.15.2:

Changes in version 1.15.1:

motifcounter

Changes in version 1.5.4:

Changes in version 1.5.3:

Changes in version 1.5.2:

Changes in version 1.5.1:

MotifDb

Changes in version 1.24:

NEW FEATURES

motifStack

Changes in version 1.25.2:

Changes in version 1.25.1:

MPRAnalyze

Changes in version 0.99.0 (2018-08-07):

MSnbase

Changes in version 2.7.12:

Changes in version 2.7.11:

Changes in version 2.7.10:

Changes in version 2.7.9:

Changes in version 2.7.8:

Changes in version 2.7.7:

Changes in version 2.7.6:

Changes in version 2.7.5:

Changes in version 2.7.4:

Changes in version 2.7.3:

Changes in version 2.7.2:

Changes in version 2.7.1:

Changes in version 2.7.0:

MSnID

Changes in version 1.15.1:

msPurity

Changes in version 1.6.1:

MSstatsTMT

Changes in version 0.99.0 (2018-09-21):

multiClust

Changes in version 1.11.2:

Changes in version 1.11.1:

mzR

Changes in version 2.15.5:

Changes in version 2.15.4:

Changes in version 2.15.3:

Changes in version 2.15.2:

Changes in version 2.15.1:

Changes in version 2.15.0:

NBSplice

Changes in version 0.99.4:

NormalyzerDE

Changes in version 0.99.24:

Changes in version 0.99.22:

Changes in version 0.99.21:

Changes in version 0.99.20:

Changes in version 0.99.19:

Changes in version 0.99.17:

Changes in version 0.99.16:

Changes in version 0.99.15:

omicplotR

Changes in version 1.1.2:

Changes in version 1.1.1:

OncoSimulR

Changes in version 2.11.1:

onlineFDR

Changes in version 0.99.7:

MODIFICATIONS

Changes in version 0.99.5:

MODIFICATIONS

oposSOM

Changes in version 2.0.1:

Changes in version 2.0.0:

ORFik

Changes in version 1.1.12:

SIGNIFICANT USER-VISIBLE CHANGES

PathoStat

Changes in version 1.8.1:

pathVar

Changes in version 1.11.2 (2018-06-29):

Changes in version 1.11.1 (2018-05-15):

pcaExplorer

Changes in version 2.8.0:

NEW FEATURES

PGA

Changes in version 1.11.4:

Changes in version 1.11.2:

phantasus

Changes in version 1.1.6:

Changes in version 1.1.5:

Changes in version 1.1.3:

Changes in version 1.1.2:

Changes in version 1.1.1:

piano

Changes in version 1.22.0:

DOCUMENTATION

Changes in version 1.20.1:

DOCUMENTATION

Pigengene

Changes in version 1.7.2 (2018-05-22):

General

plotGrouper

Changes in version 0.99.37:

New features

Changes in version 0.99.24:

New features

Changes in version 0.99.15:

New features

Changes in version 0.99.14:

Minor improvements and bug fixes

polyester

Changes in version 1.99.3:

Changes in version 1.99.2:

PowerExplorer

Changes in version 1.1.1:

Changes in version 1.1.0:

primirTSS

Changes in version 0.99.7:

pRoloc

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:

PureCN

Changes in version 1.12.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUGFIXES

qPLEXanalyzer

Changes in version 0.99.0:

qsea

Changes in version 1.7.4:

Changes in version 1.7.3:

Changes in version 1.7.2:

Changes in version 1.7.1:

RCy3

Changes in version 2.2.0:

ReactomePA

Changes in version 1.25.1:

REBET

Changes in version 0.99.0 (2018-07-12):

recount

Changes in version 1.7.5:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.7.4:

BUG FIXES

Changes in version 1.7.3:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.7.2:

BUG FIXES

Changes in version 1.7.1:

SIGNIFICANT USER-VISIBLE CHANGES

regioneR

Changes in version 1.13.2:

BUG FIXES

Changes in version 1.13.1:

NEW FEATURES

regionReport

Changes in version 1.15.4:

BUG FIXES

Changes in version 1.15.3:

BUG FIXES

Changes in version 1.15.2:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.15.1:

BUG FIXES

rGREAT

Changes in version 1.13.1:

RNASeqR

Changes in version 0.99.25:

Changes in version 0.99.24:

Changes in version 0.99.23:

RnBeads

Changes in version 1.99.0:

Changes in version 1.13.3:

Changes in version 1.13.2:

Changes in version 1.13.1:

rols

Changes in version 2.9.4:

Changes in version 2.9.3:

Changes in version 2.9.2:

Changes in version 2.9.1:

Changes in version 2.9.0:

ropls

Changes in version 1.13.8:

INTERNAL MODIFICATION

Changes in version 1.13.6:

INTERNAL MODIFICATION

Changes in version 1.13.4:

INTERNAL MODIFICATION

Changes in version 1.13.2:

BUG CORRECTION

INTERNAL MODIFICATION

rpx

Changes in version 1.17.2:

Changes in version 1.17.1:

Changes in version 1.17.0:

Rsamtools

Changes in version 1.33:

NEW FEATURES

BUG FIXES

Rsubread

Changes in version 1.32.0:

RTN

Changes in version 2.6.0:

RTNduals

Changes in version 1.6.0:

S4Vectors

Changes in version 0.20.0

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

scater

Changes in version 1.10.0:

SCBN

Changes in version 0.99.1:

scmeth

Changes in version 1.1.7:

PKG FEATURES

scPipe

Changes in version 1.3.8:

Changes in version 1.3.6:

Changes in version 1.3.5:

Changes in version 1.3.4:

Changes in version 1.3.2:

Changes in version 1.3.1:

scran

Changes in version 1.10.0:

SDAMS

Changes in version 1.1.2:

Changes in version 1.1.1:

SeqArray

Changes in version 1.21.1-1.21.7:

UTILITIES

NEW FEATURES

BUG FIXES

Changes in version 1.20.1:

BUG FIXES

seqCAT

Changes in version 1.4.0:

FEATURES

FIXES

MISCELLANEOUS:

sesame

Changes in version 1.0.0:

signeR

Changes in version 1.7.1:

SIMAT

Changes in version 1.13.1:

SIMD

Changes in version 0.99.9:

Changes in version 0.99.8:

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:

SIMLR

Changes in version 1.7.3 (2018-10-13):

simulatorZ

Changes in version 1.15.1:

SingleCellExperiment

Changes in version 1.4.0:

singleCellTK

Changes in version 1.1.26 (2018-10-23):

Changes in version 1.1.3:

Changes in version 1.1.2:

Changes in version 1.1.1:

slinky

Changes in version 0.99.0:

NEW FEATURES

SNPRelate

Changes in version 1.15.1-1.15.5:

SparseSignatures

Changes in version 1.1.4:

Changes in version 1.1.3:

statTarget

Changes in version 2.0:

NEW FEATURES

strandCheckR

Changes in version 0.99.16:

SummarizedExperiment

Changes in version 1.12.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

SWATH2stats

Changes in version 1.11.7:

UPDATE

Changes in version 1.11.6:

BUG FIXES

Changes in version 1.11.5:

UDPATE

Changes in version 1.11.4:

BUG FIXES

Changes in version 1.11.3:

BUG FIXES

Changes in version 1.11.2:

NEW FEATURES

Changes in version 1.11.1:

BUG FIXES

Changes in version 1.11.0:

NEW FEATURES

synapter

Changes in version 2.5.2:

TargetSearch

Changes in version 1.38.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

TCC

Changes in version 1.21.3:

TFEA.ChIP

Changes in version 1.1.1:

New Features:

tofsims

Changes in version 099.1:

SIGNIFICANT USER-VISIBLE CHANGES

INTERNALS

topdownr

Changes in version 1.3.6:

Changes in version 1.3.5:

Changes in version 1.3.4:

Changes in version 1.3.3:

Changes in version 1.3.2:

Changes in version 1.3.1:

Changes in version 1.3.0:

trackViewer

Changes in version 1.17.8:

Changes in version 1.17.7:

Changes in version 1.17.6:

Changes in version 1.17.4:

Changes in version 1.17.3:

Changes in version 1.17.2:

Changes in version 1.17.1:

transcriptogramer

Changes in version 1.3.6:

Changes in version 1.3.4:

Changes in version 1.3.3:

Changes in version 1.3.1:

transite

Changes in version 0.99.0:

tRNAscanImport

Changes in version 1.1.9 (2018-10-24):

Changes in version 1.1.1 (2018-08-16):

tximeta

Changes in version 0.0.16:

tximport

Changes in version 1.9.11:

Changes in version 1.9.10:

Changes in version 1.9.9:

Changes in version 1.9.6:

Changes in version 1.9.4:

Changes in version 1.9.1:

Ularcirc

Changes in version 0.99.0:

Uniquorn

Changes in version 2.1.4 (2018-10-10):

Bioconductor compliance

Changes in version 2.1.3 (2018-10-03):

Bioconductor compliance

variancePartition

Changes in version 1.11.13:

Changes in version 1.11.11:

Changes in version 1.11.10:

Changes in version 1.11.8:

Changes in version 1.11.7:

Changes in version 1.11.6:

Changes in version 1.11.5:

Changes in version 1.11.2:

Changes in version 1.11.1:

VariantAnnotation

Changes in version 1.28.0:

NEW FEATURES

BUG FIXES

xcms

Changes in version 3.3.6:

Changes in version 3.3.5:

Changes in version 3.3.4:

Changes in version 3.3.3:

Changes in version 3.3.2:

Changes in version 3.3.1:

XINA

Changes in version 1.0.0:

NEW FEATURES

BUG FIXES

xps

Changes in version 1.41:

zinbwave

Changes in version 1.3.1 (2018-05-09):

NEWS from new and existing Data Experiment Packages

celarefData

Changes in version 0.99.0 (2018-08-05):

CopyNeutralIMA

Changes in version 1.0:

dsQTL

Changes in version 2.17:

USER VISIBLE CHANGES

DuoClustering2018

Changes in version 0.1.0:

FlowSorted.Blood.EPIC

Changes in version 0.99.37 (2018-10-25):

Changes in version 0.99.36 (2018-03-24):

GIGSEAdata

Changes in version 0.99.8 (2018-06-30):

Changes in version 0.99.1 (2018-06-04):

mcsurvdata

Changes in version 1.0.1:

pRolocdata

Changes in version 1.19.4:

Changes in version 1.19.3:

Changes in version 1.19.2:

Changes in version 1.19.1:

Changes in version 1.19.0:

PtH2O2lipids

Changes in version 2016-04-21:

qPLEXdata

Changes in version 0.99.0:

RforProteomics

Changes in version 1.19.3:

Changes in version 1.19.0:

sesameData

Changes in version 1.0.0:

TabulaMurisData

Changes in version 0.99.0:

tcgaWGBSData.hg19

Changes in version 0.99.3:

PKG FEATURES

NEWS from new and existing Workflows

maEndToEnd

Changes in version 1.99.6:

Changes in version 1.99.2:

Changes in version 0.99.0:

recountWorkflow

Changes in version 1.3.1:

SIGNIFICANT USER-VISIBLE CHANGES

Deprecated and Defunct Packages

Seven software packages were removed from this release (after being deprecated in Bioc 3.7): ontoCat, spliceR, OperaMate, DASC, PAnnBuilder, phenoDist, BrowserVizDemo.

Thirteen software are deprecated in this release and will be removed in Bioc 3.9: BiocInstaller, GoogleGenomics, IrisSpatialFeatures, facopy, gaucho, nudge, RamiGO, mQTL.NMR, cytofkit, pbcmc, GeneSelector, ampliQueso, prot2D.

Three experimental data packages were removed in this release (after being deprecated in BioC 3.7): RnaSeqTutorial, cheung2010, MEALData.

Two experimental data packages are deprecated in this release and will be removed in Bioc 3.9: iontreeData, MSBdata.