October 18, 2016

Bioconductors:

We are pleased to announce Bioconductor 3.4, consisting of 1296 software packages, 309 experiment data packages, and 933 up-to-date annotation packages.

There are 101 new software packages, and many updates and improvements to existing packages; Bioconductor 3.4 is compatible with R 3.3, 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 http://bioconductor.org for details and downloads.

Contents

Getting Started with Bioconductor 3.4

To update to or install Bioconductor 3.4:

  1. Install R 3.3 (>= 3.3.1 recommended). Bioconductor 3.4 has been designed expressly for this version of R.

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

New Software Packages

There are 101 new software packages in this release of Bioconductor.

NEWS from new and existing packages

Package maintainers can add NEWS files describing changes to their packages since the last release. The following package NEWS is available:

ABAEnrichment

Changes in version 1.3.7:

NEW FEATURES

Changes in version 1.3.6:

NEW FEATURES

Changes in version 1.3.5:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

Changes in version 1.3.4:

NEW FEATURES

Changes in version 1.3.3:

BUG FIXES

affxparser

Changes in version 1.45.1 (2016-09-16):

Changes in version 1.45.0 (2015-05-03):

ALDEx2

Changes in version 1.5.2:

alpine

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 0.99.0:

AMOUNTAIN

Changes in version 0.99.1:

NEW FEATURES

USER-LEVEL CHANGES

anamiR

Changes in version 1.0.0:

Anaquin

Changes in version 0.1:

AneuFinder

Version: 1.1.6 Category: NEW FEATURES Text: Added DNAcopy algorithm to Strand-seq mode.

Version: 1.1.6 Category: SIGNIFICANT USER-LEVEL CHANGES Text: Renamed parameter ‘most.frequent.state.bivariate’ -> ‘most.frequent.state.strandseq’.

Version: 1.1.6 Category: SIGNIFICANT USER-LEVEL CHANGES Text: Renamed parameter ‘most.frequent.state.univariate’ -> ‘most.frequent.state’.

Version: 1.1.6 Category: SIGNIFICANT USER-LEVEL CHANGES Text: New parameter ‘strandseq’.

Version: 1.1.6 Category: BUG FIXES Text: Dendrogram and heatmap are now aligned properly in heatmapGenomewide().

Version: 1.1.5 Category: NEW FEATURES Text: Aneufinder runs DNAcopy algorithm in addition to the Hidden Markov Model.

Version: 1.1.5 Category: NEW FEATURES Text: New function “getQC” to get a data.frame with quality metrics.

Version: 1.1.5 Category: SIGNIFICANT USER-LEVEL CHANGES Text: Changed folder structure to include DNAcopy method.

Version: 1.1.5 Category: SIGNIFICANT USER-LEVEL CHANGES Text: Renamed methods from c(‘univariate’,’bivariate’) to c(‘HMM’,’biHMM’)

Version: 1.1.4 Category: NEW FEATURES Text: karyotypeMeasures() has new option regions.

Version: 1.1.4 Category: NEW FEATURES Text: plotHeterogeneity() for easy plotting of karyotype measures.

Version: 1.1.4 Category: NEW FEATURES Text: BiocStyle vignette.

Version: 1.1.4 Category: NEW FEATURES Text: New option use.bamsignals=FALSE/TRUE available for the binning step.

Version: 1.1.4 Category: NEW FEATURES Text: getQC() handles NULL entries as NA and is thus more robust.

Version: 1.1.4 Category: NEW FEATURES Text: complexity estimation via Michaelis-Menten is carried along.

Version: 1.1.4 Category: SIGNIFICANT USER-LEVEL CHANGES Text: Color scheme for copy number states has been improved for states >= 5-somy.

Version: 1.1.4 Category: SIGNIFICANT USER-LEVEL CHANGES Text: Option format has been removed in all functions. File format is determined automatically now.

Version: 1.1.4 Category: SIGNIFICANT USER-LEVEL CHANGES Text: clusterByQuality() clusters now on complexity as well by default.

Version: 1.1.4 Category: DEPRECATED AND DEFUNCT Text:

Version: 1.1.4 Category: BUG FIXES Text: Corrected bug in order of seqlevels after as(…, ‘GRanges’).

Version: 1.1.4 Category: BUG FIXES Text: Corrected bug in hotspotter() that caused detection of low-abundance hotspots.

AnnotationDbi

Changes in version 1.36.0:

BUG FIXES

AnnotationForge

Changes in version 1.16.0:

NEW FEATURES

MODIFICATIONS

BUG FIXES

AnnotationHub

Changes in version 2.6.0:

NEW FEATURES

MODIFICATIONS

AnnotationHubData

Changes in version 1.4.0:

NEW FEATURES

MODIFICATIONS

annotatr

Changes in version 0.99.13:

PKG FEATURES

aroma.light

Version: 3.3.2 Date: 2016-09-16 Text: BUG FIX: robustSmoothSpline() gave an error since R-devel (>= 3.4.0 r70682) (Issue #9)

Version: 3.3.2 Date: 2016-09-16 Text: Using NA_real_ (not just NA) everywhere applicable.

Version: 3.3.1 Date: 2016-08-10 Category: CLEANUP: Using seq_len() and seq_along() everywhere (Issue #8 Text:

Version: 3.3.0 Date: 2016-05-03 Text: The version number was bumped for the Bioconductor devel version, which is now BioC v3.4 for R (>= 3.3.0).

ASpli

Version: 0.98 Category: NEW FEATURES: multiple bins are reclassified using annotated junctions

attract

Version: 1.25.2 Date: 2016-10-13 - Update attract to accept MsigDB data sets in both .gmt and .gmx file formats. Before it was just .gmt files. An error is thrown if custom gene sets are not in .gmt or .gmx format. Also update attract to correct bug when you use reactome database and microarray data

Version: 1.25.1 Date: 2016-05-23 - Corrected bug found when using MsigDB data sets instead of KEGG and reactome. Also added expressionSetGeneFormat to findAttractors and calcFuncSynexprs functions. The vignette was also changed to reflect the update

BaalChIP

Changes in version 0.99.0:

NEW FEATURES

BgeeDB

Changes in version 2.0.0 (2016-10-10):

Changes in version 1.0.3 (2016-08-31):

Biobase

Changes in version 2.33:

BUG FIXES

bioCancer

Changes in version 1.0.03:

Changes in version 1.0.02:

Changes in version 1.0.01:

Changes in version 1.0.0:

BiocInstaller

Changes in version 1.24.0:

NEW FEATURES

BiocStyle

Changes in version 2.2.0:

NEW FEATURES

BUG FIXES AND IMPROVEMENTS to Bioconductor LaTeX Style 2

biomaRt

Changes in version 2.30.0:

SIGNIFICANT USER-LEVEL CHANGES

biosigner

Changes in version 1.1.14:

INTERNAL MODIFICATIONS

Changes in version 1.1.12:

INTERNAL MODIFICATIONS

Changes in version 1.1.10:

NEW FEATURE

INTERNAL MODIFICATIONS

Changes in version 1.1.8:

INTERNAL MODIFICATIONS

Changes in version 1.1.6:

INTERNAL MODIFICATIONS

Changes in version 1.1.4:

INTERNAL MODIFICATIONS

Changes in version 1.1.2:

INTERNAL MODIFICATIONS

Changes in version 1.1.0:

PACKAGE MODIFICATION

BrowserViz

Changes in version 1.9.8:

BUG FIXES

Changes in version 1.8.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

CAMERA

Changes in version 1.29.2:

BUG FIXES

Changes in version 1.29.1:

NEW FEATURES

canceR

Version: 1.5.2 - resolve issue 1 about “tl not found - delete file R/getGeneticProfiles.R - resolve ‘no visible binding for global variable - add R/aaa.R

Cardinal

Changes in version 1.5.2:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.5.1:

BUG FIXES

Changes in version 1.5.0:

NEW FEATURES

BUG FIXES

ChAMP

Changes in version 2.0.1:

Chicago

Version: 1.1.5

chipenrich

Changes in version 1.11.4:

PKG FEATURES

ChIPpeakAnno

Changes in version 3.7.9:

Changes in version 3.7.8:

Changes in version 3.7.7:

Changes in version 3.7.6:

Changes in version 3.7.5:

Changes in version 3.7.3:

Changes in version 3.7.2:

ChIPQC

Changes in version 1.9.2:

ChIPseeker

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:

ClassifyR

Changes in version 1.8.0:

clonotypeR

Changes in version 1.12.0:

OTHER CHANGES

clustComp

Changes in version 1.2.0:

clusterExperiment

Changes in version 0.99.3 (2016-07-26):

Changes

Bug fixes

Changes in version 0.99.1 (2016-05-24):

Changes

Changes in version 0.99.0 (2016-05-24):

Changes

Changes in version 0.2.0 (2016-05-10):

Changes

Changes in version 0.1.0 (2016-05-04):

Changes

Changes in version 0.0.0.9006:

Changes

Changes in version 0.0.0.9005:

Changes

Changes in version 0.0.0.9004:

Changes

clusterProfiler

Changes in version 3.1.9:

Changes in version 3.1.8:

Changes in version 3.1.7:

Changes in version 3.1.6:

Changes in version 3.1.5:

Changes in version 3.1.4:

Changes in version 3.1.3:

Changes in version 3.1.2:

Changes in version 3.1.1:

ClusterSignificance

Changes in version 1.2.0:

NEW FEATURES

CNEr

Changes in version 3.4:

NEW FEATURES

BUG FIXES

Changes in version 3.3:

BUG FIXES

NEW FEATURES

coMET

Changes in version 1.5.5 (2016-06-12):

Changes in version 1.5.3:

Changes in version 1.4.3 (2016-04-29):

compEpiTools

Changes in version 1.7.4:

Changes in version 1.7.3:

ComplexHeatmap

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:

CountClust

Changes in version 1.1.3:

crisprseekplus

Version: 0.99.0 Text:

CrispRVariants

Changes in version 1.1.6:

Changes in version 1.1.5:

Changes in version 1.1.4:

Changes in version 1.1.2:

csaw

Changes in version 1.7.4:

customProDB

Changes in version 1.13.2:

UPDATED FUNCTIONS

Changes in version 1.13.1:

BUG FIXES

NEW FEATURES

cytofkit

Changes in version 1.5.10 (2016-10-05):

MODIFICATION

Changes in version 1.5.9 (2016-10-03):

MODIFICATION

Changes in version 1.5.8 (2016-08-19):

MODIFICATION

Changes in version 1.5.7 (2016-07-13):

MODIFICATION

NEW FEATURES

Changes in version 1.5.6 (2016-07-08):

MODIFICATION

Changes in version 1.5.5 (2016-07-04):

MODIFICATION

Changes in version 1.5.4 (2016-06-14):

MODIFICATION

NEW FEATURES

CytoML

Version: 1.0.0 Category: First submission Text:

DChIPRep

Changes in version 1.3.3:

Changes in version 1.3.2:

debrowser

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:

DeepBlueR

Version: 0.99.0 Text:

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

Version: 1.9.9 Text: 10-14-2016 Lorena Pantano lorena.pantano@gmail.com Fixes: Fix the reduccion of clusters to use correlation values directly.

Version: 1.9.9 Text: 10-06-2016 Lorena Pantano lorena.pantano@gmail.com Fixes: GO enrichment function. Input genes was wrong.

Version: 1.9.7 Text: 07-29-2015 Lorena Pantano lorena.pantano@gmail.com Features: Add functions to return markdown report from DESeq2 object, and clustering function for time course data. Fixes: small bugs related to Nan values or small diversity values in QC plots.

derfinder

Changes in version 1.7.16:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.7.14:

NEW FEATURES

Changes in version 1.7.12:

BUG FIXES

Changes in version 1.7.2:

BUG FIXES

Changes in version 1.7.1:

SIGNIFICANT USER-VISIBLE CHANGES

derfinderPlot

Changes in version 1.7.10:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.7.8:

BUG FIXES

Changes in version 1.7.1:

SIGNIFICANT USER-VISIBLE CHANGES

DESeq2

Changes in version 1.13.8:

Changes in version 1.13.3:

DiffBind

Changes in version 2.2.0:

diffHic

Changes in version 1.5.6:

Director

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:

DOSE

Changes in version 2.11.12:

Changes in version 2.11.11:

Changes in version 2.11.10:

Changes in version 2.11.9:

Changes in version 2.11.8:

Changes in version 2.11.7:

Changes in version 2.11.6:

Changes in version 2.11.5:

Changes in version 2.11.4:

Changes in version 2.11.3:

Changes in version 2.11.2:

Changes in version 2.11.1:

EBImage

Changes in version 4.16.0:

SIGNIFICANT USER-VISIBLE CHANGES

PERFORMANCE IMPROVEMENTS

edgeR

Changes in version 3.16.0:

EGSEA

Changes in version 1.1.10:

Changes in version 1.1.9 (2016-08-19):

Changes in version 1.1.8 (2016-07-12):

Changes in version 1.1.7 (2016-06-30):

Changes in version 1.1.6 (2016-05-31):

Changes in version 1.1.5 (2016-05-27):

Changes in version 1.1.4 (2016-05-23):

Changes in version 1.1.1 (2016-05-10):

ENmix

Changes in version 1.9.4:

Changes in version 1.9.3:

Changes in version 1.9.2:

Changes in version 1.9.1:

EnrichedHeatmap

Changes in version 1.3.5:

Changes in version 1.3.4:

EnrichmentBrowser

Changes in version 2.3.2:

ensembldb

Changes in version 1.5.14:

NEW FEATURES

Changes in version 1.5.13:

NEW FEATURES

Changes in version 1.5.12:

USER VISIBLE CHANGES

BUG FIXES

Changes in version 1.5.11:

BUG FIXES

Changes in version 1.5.10:

USER VISIBLE CHANGES

Changes in version 1.5.9:

NEW FEATURES

Changes in version 1.5.8:

BUG FIXES

Changes in version 1.5.7:

OTHER CHANGES

Changes in version 1.5.6:

BUG FIXES

Changes in version 1.5.5:

BUG FIXES

Changes in version 1.5.4:

Bug fixes

Changes in version 1.5.2:

NEW FEATURES

Changes in version 1.5.1:

BUG FIXES

ensemblVEP

Changes in version 1.14.0:

NEW FEATURES

epivizrData

Changes in version 999.999:

epivizrServer

Changes in version 999.999:

epivizrStandalone

Changes in version 999.999:

erccdashboard

Changes in version 1.7.2:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES AND MINOR IMPROVEMENTS

Changes in version 1.7.1:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES AND MINOR IMPROVEMENTS

esetVis

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:

ExperimentHub

Version: 1.0.0 Category: Package added to release BioC 3.4 Text:

ExperimentHubData

Version: 1.0.0 Category: Package added to release BioC 3.4 Text:

fgsea

Changes in version 0.99.8:

Changes in version 0.99.7:

Changes in version 0.99.6:

Changes in version 0.99.5:

FindMyFriends

Changes in version 1.3.3:

FitHiC

Version: 0.99.0 Text:

Version: 0.99.1 Text: grammar in FitHiC.R

Version: 0.99.2 Text: benjamini_hochberg_correction in R

Version: 0.99.3 Text:

Version: 0.99.4 Text:

Version: 0.99.5 Text: vignettes

flowCL

Version: 1.11.1 Text:

Version: 1.11.2 Text:

flowDensity

Version: 1.7.1 Text:

flowPloidy

Changes in version 0.99.3 (2016-10-17):

Internal Changes

Changes in version 0.99.2 (2016-10-12):

Internal Changes

Changes in version 0.99.1 (2016-10-11):

User Visible Changes

Internal Changes

Changes in version 0.99.0 (2016-08-25):

flowQB

Changes in version 2.1.1:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.21.0:

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

Changes in version 1.20.1:

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

FunChIP

Version: 0.99.0 Text:

Version: 0.99.3 Text:

Version: 0.99.4 Text:

gCMAP

Changes in version 1.17.3:

Changes in version 1.17.2:

Changes in version 1.17.0:

gCMAPWeb

Changes in version 1.13.3:

Changes in version 1.13.1:

gCrisprTools

Version: 0.99.0 Category: Initial bioconductor submission. Text:

gdsfmt

Changes in version 1.10.0:

Changes in version 1.8.0-1.8.3:

geecc

Changes in version 1.7.7 (2016-09-19):

GEM

Changes in version 0.99.3 (2016-05-24):

MODIFICATION

Changes in version 0.99.2 (2016-05-21):

MODIFICATION

Changes in version 0.99.1 (2016-05-16):

MODIFICATION

genbankr

Changes in version 1.1.5:

MINOR CHANGES

Changes in version 1.1.4:

BUGFIXES

Changes in version 1.1.3:

BUGFIXES

GeneNetworkBuilder

Changes in version 1.15.2:

geneplast

Changes in version 1.0.0:

GeneticsPed

Changes in version 2007-09-12:

Changes in version 2007-04-25:

Changes in version 2007-04-19:

Changes in version 2007-04-18:

Changes in version 2007-04-06:

Changes in version 2007-04-01:

Changes in version 2007-04:

Changes in version 2007-03-02:

Changes in version 2006-03-29:

Changes in version 2006-03-16:

genomation

Changes in version 1.5.6:

NEW FUNCTIONS AND FEATURES

Changes in version 1.5.5:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.5.4:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.5.3:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.5.2:

IMPROVEMENTS AND BUG FIXES

GenomeInfoDb

Changes in version 1.10.0:

NEW FEATURES

DEPRECATED AND DEFUNCT

MODIFICATIONS

BUG FIXES

GenomicAlignments

Changes in version 1.10.0:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

GenomicFeatures

Version: 1.26 Category: NEW FEATURES Text: makeTxDbFromGRanges() now recognizes features of type lnc_RNA, antisense_lncRNA, transcript_region, and pseudogenic_tRNA, as transcripts.

Version: 1.26 Category: NEW FEATURES Text: Add ‘intronJunctions’ argument to mapToTranscripts().

Version: 1.26 Category: SIGNIFICANT USER-VISIBLE CHANGES Text:

Version: 1.26 Category: DEPRECATED AND DEFUNCT Text: The ‘vals’ argument of the “transcripts”, “exons”, “cds”, and “genes” methods for TxDb objects is now defunct (was deprecated in BioC 3.3).

Version: 1.26 Category: DEPRECATED AND DEFUNCT Text: The “species” method for TxDb object is now defunct (was deprecated in BioC 3.3).

Version: 1.26 Category: BUG FIXES Text:

GenomicRanges

Version: 1.26.0 Category: NEW FEATURES Text: Add ‘with.revmap’ argument to “reduce” method for GRangesList objects.

Version: 1.26.0 Category: NEW FEATURES Text: Add ‘with.revmap’ argument to various “disjoin” methods.

Version: 1.26.0 Category: NEW FEATURES Text: makeGRangesFromDataFrame() now tries to turn the “start” and “end” columns of the input data frame into numeric vectors if they are not already.

Version: 1.26.0 Category: NEW FEATURES Text: Add makeGRangesListFromDataFrame() function.

Version: 1.26.0 Category: NEW FEATURES Text: Add “summary” method for GenomicRanges objects.

Version: 1.26.0 Category: NEW FEATURES Text: Add ‘use.names’ argument to the granges(), grglist(), and rglist() generics and methods, as well as to a bunch of “ranges” methods (for GRanges, GPos, GNCList, GRangesList, and DelegatingGenomicRanges). Default is TRUE to preserve existing behavior.

Version: 1.26.0 Category: NEW FEATURES Text: Add ‘use.mcols’ arguments to the “ranges” methods for GPos objects.

Version: 1.26.0 Category: SIGNIFICANT USER-LEVEL CHANGES Text:

Version: 1.26.0 Category: DEPRECATED AND DEFUNCT Text:

Version: 1.26.0 Category: BUG FIXES Text: Fix bug in distanceToNearest() related to ranges starting at zero.

Version: 1.26.0 Category: BUG FIXES Text: Fix GRanges(Seqinfo()).

GenRank

Version: 1.0.3 Category: Made slight modifications to the vignette and added a couple of figures. Changed the way RankProduct method handles the missing evidence across evidence layers Text:

GenVisR

Changes in version 1.1.5:

ggtree

Changes in version 1.5.17:

Changes in version 1.5.16:

Changes in version 1.5.15:

Changes in version 1.5.14:

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:

Glimma

Changes in version 1.2.0:

Changes in version 1.1.0:

globalSeq

Changes in version 1.1.0 (2016-10-18):

GOexpress

Changes in version 1.7.1:

GENERAL UPDATES

GOpro

Version: 0.99.2 Text:

GOSemSim

Changes in version 1.99.4:

Changes in version 1.99.3:

Changes in version 1.99.2:

Changes in version 1.99.1:

Changes in version 1.99.0:

Changes in version 1.31.2:

Changes in version 1.31.1:

gprege

Changes in version 1.17.1 (2016-10-07):

GSALightning

Version: 1.1.1 Category: Codes Text:

Version: 1.1.1 Category: Added “maxmean” statistics Text:

Version: 1.1.1 Category: Added “wilcoxTest” for Mann-Whitney-U tests for single gene analysis Text:

Version: 1.1.1 Category: Default for GSALight() is now “maxmean” with restandardization Text:

Version: 1.1.1 Category: Fix some issues to make GSALight() equivalent to GSA of Efron and Tibshirani Text:

Version: 1.1.1 Category: The target gene list is now a list instead of a data table Text:

Version: 1.1.1 Category: The Vignette now contains a comprehensive user guide Text:

Version: 1.1.1 Category: All documentations are updated accordingly Text:

Version: 1.1.2 Category: Added “importFrom(“stats”, “p.adjust”, “rbinom”, “var”, “wilcox.test”)” to NAMESPACE Text:

Version: 1.1.2 Category: Import “stats” in description Text:

Version: 1.1.2 Category: Added back manual for “wilcoxTest Text:

Version: 1.1.3 Category: Bioconductor version updates Text:

Version: 1.1.5 Category: Updated references and manual and vignette Text:

Version: 1.1.5 Category: Added Github URL Text:

Version: 1.1.6 Category: Fixed default settings of permTestLight() by adding match.args and setting nperm=NULL Text:

GSAR

Changes in version 1.8.0:

GSEABase

Changes in version 1.35:

BUG FIXES

Guitar

Changes in version 1.11.9:

GWASTools

Changes in version 1.19.1:

Harman

Changes in version 1.2.0:

Changes in version 1.0.2:

HDTD

Changes in version 1.7.1 (2016-09-15):

hiAnnotator

Changes in version 1.7.1:

HIBAG

Changes in version 1.10.0:

Changes in version 1.9.0-1.9.3:

Changes in version 1.8.0-1.8.3:

hiReadsProcessor

Changes in version 1.9.3:

Changes in version 1.9.1:

HiTC

Changes in version 1.17.1:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

hpar

Changes in version 1.15.3:

Changes in version 1.15.2:

Changes in version 1.15.1:

Changes in version 1.15.0:

HTSFilter

Changes in version 1.13.1:

illuminaio

Changes in version 0.15.1 (2016-08-27):

Changes in version 0.15.0 (2015-05-03):

InPAS

Changes in version 1.5.7:

NEW FEATURE

Changes in version 1.5.6:

NEW FEATURE

Changes in version 1.5.5:

NEW FEATURE

Changes in version 1.5.4:

NEW FEATURE

BUG FIXES

Changes in version 1.5.1:

NEW FEATURE

BUG FIXES

InteractionSet

Changes in version 1.1.6:

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:

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USER VISIBLE CHANGES

IRanges

Changes in version 2.8.0:

NEW FEATURES

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DEPRECATED AND DEFUNCT

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isobar

Changes in version 1.19.1:

isomiRs

Changes in version 1.1.5:

OTHERS

Changes in version 1.1.4:

OTHERS

Changes in version 1.1.2:

OTHERS

IVAS

Changes in version 1.5.1:

JunctionSeq

Changes in version 1.3.4:

Minor bugfixes

kebabs

Changes in version 1.7.3:

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kimod

Version: 1.1.1 Text:

LedPred

Version: 1.7.4 Text: Deals with error when at least one feature in some training fold of the ModelPerformance CV algo has all value zero -> removes it

Version: 1.7.3 Text: Fixed opposite sign of feature weigths in some situations

Version: 1.7.3 Text: LedPred function returns object with many more informations

Version: 1.7.1 Category: Hotfix: Fixed sign of prediction Text:

limma

Changes in version 3.30.0:

LINC

Changes in version 1.1.6:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

BUG FIXES

LOBSTAHS

Changes in version 2016-04-21:

M3D

Version: 1.7.4 Text:

Version: 1.7.5 Text:

Version: 1.7.11 Text:

Version: 1.7.12 Text:

maftools

Changes in version 0.99.50:

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NON SIGNIFICANT CHANGES

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Changes in version 0.99.32:

NON SIGNIFICANT CHANGES

Changes in version 0.99.31:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

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DEPRECATED AND DEFUNCT

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NEW FEATURES

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NEW FEATURES

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CHANGES

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CHANGES

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CHANGES

MANOR

Changes in version 2014-10-01:

Changes in version 2013-07-03 (2013-07-03):

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matter

Changes in version 0.99.11 (2016-10-11):

BUG FIXES

Changes in version 0.99.10 (2016-10-11):

SIGNIFICANT USER-VISIBLE CHANGES

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NEW FEATURES

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SIGNIFICANT USER-VISIBLE CHANGES

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BUG FIXES

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BUG FIXES

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BUG FIXES

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Changes in version 0.99.3:

BUG FIXES

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BUG FIXES

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BUG FIXES

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BUG FIXES

Changes in version 0.6:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

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SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

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NEW FEATURES

Changes in version 0.2:

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SIGNIFICANT USER-VISIBLE CHANGES

meshes

Changes in version 0.99.7:

Changes in version 0.99.6:

Changes in version 0.99.3:

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Changes in version 0.99.1:

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Changes in version 0.0.1:

MeSHSim

Version: 2015-01-12 Text:

Version: 2015-01-12 Text:

Version: 2015-01-12 Text:

Version: 2015-01-12 Text:

Version: 2015-01-12 Text:

Version: 2015-01-11 Text:

Version: 2015-01-08 Text:

Version: 2014-12-14 Text:

Version: 2014-11-16 Text:

metabomxtr

Changes in version 1.7.1:

MetaboSignal

Changes in version 1.0.0:

SIGNIFICANT USER-VISIBLE CHANGES

NEW FEATURES

metagenomeFeatures

Changes in version 1.1.3 (2016-10-01):

Changes in version 1.1.2 (2016-03-26):

metagenomeSeq

Changes in version 1.15:

MetCirc

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:

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Changes in version 0.98.0:

methylKit

Version: 0.99.4 Category: IMPROVEMENTS AND BUG FIXES Text: all annotation functions are now removed and are available through genomation package. See the vignette for examples. Most functions have similar names and functionality in genomation. The users need to convert methylKit objects to GRanges using as(methylKit.obj,”GRanges”) before they can use genomation functions.

Version: 0.99.3 Category: IMPROVEMENTS AND BUG FIXES Text: Fixed a bug in processBismark() C++ function where BAM files are should be treated as 0-based. Now this is fixed.

Version: 0.99.3 Category: IMPROVEMENTS AND BUG FIXES Text: Bug in calculateDiffMethDSS is fixed (https://github.com/al2na/methylKit/issues/49)

Version: 0.99.2 Category: IMPROVEMENTS AND BUG FIXES Text: Fixed a bug in methRead() introduced after the addition of mincov argument. the bug occurred only reading files legacy text files that have CpGs with coverage below 10

Version: 0.99.2 Category: IMPROVEMENTS AND BUG FIXES Text: Changes to vignette for better description of the tests.

Version: 0.99.2 Category: IMPROVEMENTS AND BUG FIXES Text: Compiler error that occurs in older compilers are fixed via this PR https://github.com/al2na/methylKit/pull/43

Version: 0.99.1 Category: IMPROVEMENTS AND BUG FIXES Text: mostly changes to meet BioCcheck() requirements and reccomendations

Version: 0.99.1 Category: IMPROVEMENTS AND BUG FIXES Text: C++ code compiles on windows now, regex requirement is no longer there.

Version: 0.9.6 Category: IMPROVEMENTS AND BUG FIXES Text: changes to following function names: read() to methRead() read.bismark to processBismarkAln() adjust.methylC() to adjustMethylC() get.methylDiff() to getMethylDiff() annotate.WithFeature() to annotateWithFeature() annotate.WithFeature.Flank() to annotateWithFeatureFlank() annotate.WithGenicParts() to annotateWithGenicParts() read.bed() to readBed() read.feature.flank() to readFeatureFlank() read.transcript.features() to readTranscriptFeatures()

Version: 0.9.6 Category: IMPROVEMENTS AND BUG FIXES Text: Improved documentation for methRead() (old read())

Version: 0.9.6 Category: IMPROVEMENTS AND BUG FIXES Text: Now, bismark cytosine report and coverage files can be read using methRead() pipeline argument. see ?methRead

Version: 0.9.6 Category: IMPROVEMENTS AND BUG FIXES Text: Ported the Perl script for methylation base calling to C/C++ via Rcpp. Contributed by Alexander Gosdschan.

Version: 0.9.6 Category: IMPROVEMENTS AND BUG FIXES Text: methRead() uses data.table::fread() to read files faster.

Version: 0.9.6 Category: IMPROVEMENTS AND BUG FIXES Text: methRead() has a new argument mincov, which sets the minimum number of reads that needs to cover a base. Positions with coverage below this number are discarded.

Version: 0.9.6 Category: NEW FUNCTIONS AND FEATURES Text: new function methSeg() can segment methylation (methylRaw objects) and differential methylation (methylDiff objects) profiles to segments. Associated function methSeg2bed() creates BED files from segments. see ?methSeg. A test is added to check this in R CMD check. Contributed by Arsene Wabo and Alexander Gosdschan.

Version: 0.9.6 Category: NEW FUNCTIONS AND FEATURES Text: new tabix based classes methylRawDB, methylRawListDB, methylBaseDB, methylDiffDB and respective methods implemented. Tests are updated to check proper function in R CMD check. Contributed by Alexander Gosdschan.

Version: 0.9.6 Category: NEW FUNCTIONS AND FEATURES Text: calculateDiffMeth() now supports basic overdispersion correction and multiple methods for pvalue correction. The function also now handles covariates such as age,sex etc. A test is added to check this in R CMD check. Contributed by Adrian Bierling.

Version: 0.9.6 Category: NEW FUNCTIONS AND FEATURES Text: New function calculateDiffMethDSS() is using beta-binomial model from DSS package to calculate differential methylation. Contributed by Dhruva Chandramohan with modifications from Altuna Akalin. This is a modified version of the function from DSS package so that it can work with methylKit objects.

Version: 0.9.6 Category: NEW FUNCTIONS AND FEATURES Text: dataSim creates a methylBase object with simulated methylation data. A test is added to check this in R CMD check. Contributed by Adrian Bierling.

Version: 0.9.5 Category: IMPROVEMENTS AND BUG FIXES Text: travis CI build shield added

Version: 0.9.4 Category: IMPROVEMENTS AND BUG FIXES Text: tileMethylCounts now works on methylBase objects, affected by BioC 3.0 upgrade. A test is added to check this in R CMD check.

Version: 0.9.3 Category: IMPROVEMENTS AND BUG FIXES Text: compatibility with BioC 3.0. Multiple BioC functions moved to other packages within BioC,which broke some code and caused installation issues. Now this is fixed.

Version: 0.9.3 Category: IMPROVEMENTS AND BUG FIXES Text: data.table::merge is now stable when all=TRUE. Removed my(altuna) version of data.table::merge the code base.

Version: 0.9.2.5 Category: IMPROVEMENTS AND BUG FIXES Text: calculateDiffMeth slim=FALSE argument works correctly when there are multiple samples per group.

Version: 0.9.2.4 Category: IMPROVEMENTS AND BUG FIXES Text: install_github() now works correctly. Removed blank lines at the end of DESCRIPTION file.

Version: 0.9.2.4 Category: IMPROVEMENTS AND BUG FIXES Text: calculateDiffMeth and tileMethylCounts now works correctly, typos were introduced in code with 0.9.2.2. Now these are fixed

Version: 0.9.2.3 Category: IMPROVEMENTS AND BUG FIXES Text: regionCounts() bug occurring when the first argument is a class of methylBase is fixed. The bug introduced an additional column to the resulting methylBase object. https://groups.google.com/forum/#!topic/methylkit_discussion/p19K-pgavAI

Version: 0.9.2.2 Category: IMPROVEMENTS AND BUG FIXES Text: unite() issues when destrand=FALSE is resolved. The issue appeared due to numeric vs. integer conflict when merging data sets using chr,start and end locations.

Version: 0.9.2.2 Category: IMPROVEMENTS AND BUG FIXES Text: typo in calculateDiffMeth() argument “weighted.mean” is fixed.

Version: 0.9.2.2 Category: IMPROVEMENTS AND BUG FIXES Text: unite() is faster when destrand=TRUE, due to improvements in internal function .CpG.dinuc.unify()

Version: 0.9.2.2 Category: IMPROVEMENTS AND BUG FIXES Text: regionCounts() strand.aware argument now works correctly. This bug had no effect on tileMethylCounts. With the default arguments, strand aware setting was not in effect at all, so every region was treated as strandless.

Version: 0.9.2.2 Category: IMPROVEMENTS AND BUG FIXES Text: Conversion to GRanges objects now removes seqlevels(chromosome names) that are not used. Not removing these could cause problems in regionCounts() function and functions depending on regionCounts().

Version: 0.9.2.2 Category: IMPROVEMENTS AND BUG FIXES Text: read() function in some cases was treating strand columns of the flat CpG files as logical if strand had F or R letters and most of the first CpGs were having F strand (Forward strand). Now this is fixed.

Version: 0.9.2.1 Category: IMPROVEMENTS AND BUG FIXES Text: Fixes a bug in getMethylationStats() function that generates incorrect label numbers when the user overrides the default number of breaks for the histogram. Contributed by Bonnie Barrilleaux.

Version: 0.9.2 Category: IMPROVEMENTS AND BUG FIXES Text: A bug introduced with 0.9.1 is fixed. The bug occured when unite() function

Version: 0.9.2 Category: is used with destrand=TRUE argument. It returned less number of CpGs then it was Text:

Version: 0.9.2 Category: supposed to, although returned CpGs had correct methylation and coverage values Text:

Version: 0.9.1 Category: NEW FUNCTIONS AND FEATURES Text: objects takes less memory and they are reorganized. updateMethObject() updates the objects from previous versions the latest version.

Version: 0.9.1 Category: NEW FUNCTIONS AND FEATURES Text: New batch effect control functions are implemented. You can control if certain principal components are associated with batch effects and remove those components from your data. see ?assocComp amd ?removeComp. In addition, if you have corrected for the batch effects via other methods, you can reconstruct a corrected methylBase object ( see ?reconstruct). Check the “batch effects” section in the vignette.

Version: 0.9.1 Category: IMPROVEMENTS AND BUG FIXES Text: unite() function takes less time due to use of data.table::merge

Version: 0.9.1 Category: IMPROVEMENTS AND BUG FIXES Text: fixes a bug appeared with R 3.02, where getting exon and intron coordinates from BED12 files produced an error.

Version: 0.9.1 Category: IMPROVEMENTS AND BUG FIXES Text: tested with R 3.2 and matching bioconductor packages

Version: 0.9.1 Category: IMPROVEMENTS AND BUG FIXES Text: data(methylKit) has the new objects

Version: 0.5.7 Category: IMPROVEMENTS AND BUG FIXES Text: tested with R 3.0 and matching bioconductor packages

Version: 0.5.7 Category: IMPROVEMENTS AND BUG FIXES Text: deprecated matchMatrix import from IRanges was causing a problem with package installation. v0.5.7 fixes that problem.

Version: 0.5.7 Category: IMPROVEMENTS AND BUG FIXES Text: Now there is no need for “chr” string in BED files when reading them as annotation files. Some assemblies do not have the “chr”” string in their chromosome names.

Version: 0.5.6 Category: NEW FUNCTIONS AND FEATURES Text: new arguments for clusterSamples() and PCASamples() functions are added. With the new options “sd.filter”,”sd.threshold”,”filterByQuantile” are added. These options help finetune how low variation bases/regions are discarded prior to clustering or PCA. See ?PCASamples and ?clusterSamples() for details on the new options

Version: 0.5.6 Category: NEW FUNCTIONS AND FEATURES Text: FAQ section added to the vignette

Version: 0.5.6 Category: NEW FUNCTIONS AND FEATURES Text: show methods added for each class. Now, typing the variable name containing the object will display concise information about the contents of the object.

Version: 0.5.6 Category: NEW FUNCTIONS AND FEATURES Text: Subsetting objects via “[” notation is now enabled. You can subset rows of the objects and it will return a new object rather than just a data frame.

Version: 0.5.6 Category: IMPROVEMENTS AND BUG FIXES Text: tileMethylCounts() error is fixed. Error occurred when tilling sparsely covered small chromosomes like chrM in human RRBS data.

Version: 0.5.6 Category: IMPROVEMENTS AND BUG FIXES Text: read.bismark() can deal with Bismark output with Bowtie2. Bowtie2 can put gaps in the alignment, now read.bismark() can deal with those gaps when parsing the SAM file.

Version: 0.5.6 Category: IMPROVEMENTS AND BUG FIXES Text: Coverage columns are coerced to integer when reading generic methylation per base files. BSMAP scripts can produce a methylation ratio file where coverages (or “effective CT counts” as they are called) are not always integers, which causes a problem in the downstream analysis. Now, these non-integer columns are rounded to nearest integer while reading. See http://zvfak.blogspot.com/2012/10/how-to-read-bsmap-methylation-ratio.html for example usage of this functionality.

Version: 0.5.5 Category: IMPROVEMENTS AND BUG FIXES Text: Differential methylation percentage calculation bug fixed. The bug occurred when “min.per.group” argument used in unite() function and when “weighted.mean=TRUE” in calculateDiffMeth() function.

Version: 0.5.5 Category: IMPROVEMENTS AND BUG FIXES Text: plotTargetAnnotation bug is fixed. Bug occured when “precedence” argument set to FALSE.

Version: 0.5.4 Category: IMPROVEMENTS AND BUG FIXES Text: Examples added to help pages

Version: 0.5.4 Category: IMPROVEMENTS AND BUG FIXES Text: Changes to DESCRIPTION for complying with the bioconductor guidelines

Version: 0.5.4 Category: IMPROVEMENTS AND BUG FIXES Text: unused “cor” option removed from PCASamples() function

Version: 0.5.4 Category: IMPROVEMENTS AND BUG FIXES Text: some irrelevant functions are not exported (i.e they are not public) anymore.

Version: 0.5.4 Category: IMPROVEMENTS AND BUG FIXES Text: getContext() looks for the correct slot name now

Version: 0.5.3 Category: NEW FUNCTIONS AND FEATURES Text: new function adjust.methylC() can be used to adjust measured 5mC levels by measured 5hmC levels

Version: 0.5.3 Category: IMPROVEMENTS AND BUG FIXES Text: pool() function bug fixed where one of the groups have one sample the pool function was not returning correct values

Version: 0.5.3 Category: IMPROVEMENTS AND BUG FIXES Text: calculateMethDiff() function option “SLIM” is now working. If set to TRUE SLIM method for q-value calculation will be used. If FALSE, p.adjust with method=”BH” option will be used for P-value correction.

Version: 0.5.3 Category: IMPROVEMENTS AND BUG FIXES Text: read.bismark() function now works correctly under Windows.

Version: 0.5.3 Category: IMPROVEMENTS AND BUG FIXES Text: read.bismark() bug occurring when the reads are paired and overlapping is fixed now.

Version: 0.5.3 Category: IMPROVEMENTS AND BUG FIXES Text: read.bismark() bug occurring when the alignment is done in non-directional manner is fixed now. However, illumina sequencing protocols are directional and you are unlikely to have encountered this error if you aligned your sequences in a directional manner.

Version: 0.5.3 Category: IMPROVEMENTS AND BUG FIXES Text: getCorrelation() function has a new option called “method” can take the value of “spearman”,”person” or “kendall”

Version: 0.5.2 Category: NEW FUNCTIONS AND FEATURES Text: new function pool() sums up coverage, numCs and numTs values within each group so one representative sample for each group will be created in a new methylBase object.

Version: 0.5.2 Category: NEW FUNCTIONS AND FEATURES Text: new function normalizeCoverage() normalizes coverage and associated number of Cs and number of Ts values between samples using a scaling factor derived from the ratio between mean or median of coverage distributions of samples.

Version: 0.5.1 Category: IMPROVEMENTS AND BUG FIXES Text: calculateDiffMeth() can now deal with differential methylation calculations where one group has multiple samples but the other one has only one.

Version: 0.5 Category: NEW FUNCTIONS AND FEATURES Text: new function reorganize() can be used to reorganize methylRawList and methylBase objects to create new objects from subset of samples or can be used to change the order of samples and treatment vector.

Version: 0.5 Category: NEW FUNCTIONS AND FEATURES Text: new function bedgraph() can output UCSC bedgraph files for methylRaw and methylDiff objects

Version: 0.5 Category: NEW FUNCTIONS AND FEATURES Text: new function percMethylation() extracts percent methylation values from a methylBase object and returns a matrix

Version: 0.5 Category: NEW FUNCTIONS AND FEATURES Text: unite() now can merge bases/regions that are not covered by all samples by setting “min.per.group” option

Version: 0.5 Category: NEW FUNCTIONS AND FEATURES Text: PCASamples() has new options “transpose” and “sd.threshold”. Now, one can do PCA analysis on the transposed % methylation values. “sd.threshold” is for removing rows with small variation prior to PCA analysis .see ?PCASamples for details

Version: 0.5 Category: IMPROVEMENTS AND BUG FIXES Text: regionCounts() bug that appeared with data.table 1.8.0 is fixed

Version: 0.5 Category: IMPROVEMENTS AND BUG FIXES Text: unite() bug that appeared with R 2.15 is fixed

Version: 0.5 Category: IMPROVEMENTS AND BUG FIXES Text: calculateDiffMeth() can deal with NA values introduced by setting “min.per.replicate” option of unite() function

Version: 0.5 Category: IMPROVEMENTS AND BUG FIXES Text: PCASamples() now uses “prcomp” function to do the PCA analysis

Version: 0.5 Category: IMPROVEMENTS AND BUG FIXES Text: external annotation data (cpgi.hg18.bed.txt and refseq.hg18.bed.txt) that comes with the package is now only a subset of full datasets. Do not use them for your own analysis, download the complete annotation data from UCSC or other sources in BED format.

Version: 0.4.1 Category: NEW FUNCTIONS AND FEATURES Text: new function select() can be used to subset methylRaw, methylBase and methylDiff objects to create new objects with a subset of methylation data useful if you want to use only a particular portion of methylation events on the genome.

Version: 0.4.1 Category: IMPROVEMENTS AND BUG FIXES Text: read.bismark bug fixed, now it should be able to save methylation call files with no problem

Version: 0.4 Category: NEW FUNCTIONS AND FEATURES Text: New read.bismark() function can read directly from a sorted SAM file output by Bismark aligner, the function can save methylation calls as text files or read them as methylRaw object to be used in analysis

Version: 0.4 Category: NEW FUNCTIONS AND FEATURES Text: calculateDiffMeth() can do all differential methylation calculations using multiple-cores if ‘num.cores’ is set to an integer denoting how many cores should be used.

Version: 0.4 Category: NEW FUNCTIONS AND FEATURES Text: getCoverageStats() & getMethylationStats() have a new option called ‘labels’, if set to FALSE, no labels will be drawn on top of the histogram bars.

Version: 0.4 Category: IMPROVEMENTS AND BUG FIXES Text: cov.bases option in tileMethylCounts() now works

Version: 0.4 Category: IMPROVEMENTS AND BUG FIXES Text: methylRaw,methylBase and methylDiff objects have a new slot ‘resolution’, which designates whether methylation information is base-pair resolution or regional resolution. allowed values ‘base’ or ‘region’

Version: 0.4 Category: IMPROVEMENTS AND BUG FIXES Text: getCoverageStats() & getMethylationStats() now print the sample ids and methylation context automatically in the title when plotting

Version: 0.4 Category: IMPROVEMENTS AND BUG FIXES Text: getCoverageStats() & getMethylationStats() takes extra options to be passed to hist() function

Version: 0.4 Category: IMPROVEMENTS AND BUG FIXES Text: destrand option of unite() function will be over-ridden when methylRawList to be united contains regions rather than bases

Version: 0.4 Category: IMPROVEMENTS AND BUG FIXES Text: unite() function checks if supplied elements of methylRawList object have the same context,assembly and resolution before uniting data sets.

Version: 0.4 Category: IMPROVEMENTS AND BUG FIXES Text: validity function checking the format of the data for a methylRaw object is implemented

Version: 0.4 Category: IMPROVEMENTS AND BUG FIXES Text: clusterSamples() and PCASamples() take methylation context information automatically and use it in plot titles

Version: 0.3.1 Category: IMPROVEMENTS AND BUG FIXES Text: syntax error when fisher.test applied at calculateMethDiff() is fixed.

MGFR

Changes in version 0.99.2:

minfi

Changes in version 1.19:

miRcomp

Changes in version 1.3.3:

mirIntegrator

Version: 1.3.1 Category: The warning message fixed: “Removed 3 rows containing missing values (geom_path).” Text:

Version: 1.3.1 Category: microRNAadded <- microRNAadded[complete.cases(microRNAadded Text:

Version: 1.3.1 Category: Plots were improved on this version Text:

miRNAmeConverter

Changes in version 1.1.6:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

BUG FIXES

miRNAtap

Changes in version 1.7.2:

missMethyl

Changes in version 1.7.3:

MLP

Changes in version 1.21.1:

MODA

Changes in version 0.99.4:

NEW FEATURES

USER-LEVEL CHANGES

BUG FIXES

monocle

Version: 2.0.0 Text:

Version: 2.1.1 Category: BUGFIXES Text: Fixed an problem where reduceDimension would return different results on repeated runs given the same inputs.The problem was actually in DDRTree in two places: kmeans and irlba. We now call irlba with deterministically initialized eigenvectors and kmeans with deterministically selected rows of the input.

Version: 2.1.1 Category: BUGFIXES Text: Fixed a problem in classifyCells related to joining factors and levels. This would generate annoying warnings.

Version: 2.1.1 Category: BUGFIXES Text: Fixed the check for valid sizeFactors prior to differentialGeneTest. Without this check, differentialGeneTest would report FAIL on all genes because of factors not having enough levels.

Version: 2.1.0 Category: FEATURES Text: Monocle’s algorithm for converting relative expression values (e.g. TPMs) into absolute transcript counts, called “Census” has been re-designed. The new version is much more accurate. Census is available through the relative2abs() function. The interface to this function has changed, and the output values will be quite different from the old version. The main change is that the version in 1.99.0 reported cDNA counts, as estimated in each cell’s cDNA library. Now, relative2abs reports estimates of mRNA counts in the lysate. These are easier to compare with experiments that estimate mRNA counts via the use of spike-in controls.

Version: 2.1.0 Category: FEATURES Text: A new heatmap function plot_pseudotime_heatmap() replaces the old plot_genes_heatmap().

Version: 2.1.0 Category: FEATURES Text: Lots of new documentation. More to follow in upcoming releases.

Version: 2.1.0 Category: BUGFIXES Text: Ordering cells with DDRTree no longer compresses cells at the tips of trajectories.

Version: 2.1.0 Category: BUGFIXES Text: Pseudo counts are now applied correctly no matter what the underlying distribution used to model expression is.

Version: 2.1.0 Category: BUGFIXES Text: Variance stabilization is applied correctly when a CellDataSet object’s expressionFamily is negbinomial.size().

Version: 2.1.0 Category: BUGFIXES Text: The gene_id field in results from calculateMarkerSpecificity is now a character instead of a factor. This was leading to indexing errors and nonsensical semi-supervised clustering and ordering results.

Version: 2.1.0 Category: BUGFIXES Text: BEAM() and plot_branched_heatmap() now use cBind instead of cbind, fixing an issue with sparse matrices.

Version: 1.99.0 Text: The first public release of the Monocle 2 series. For a summary of new features and changes, please see: http://cole-trapnell-lab.github.io/monocle-release/features/

msa

Changes in version 1.5.5:

Changes in version 1.5.4:

Changes in version 1.5.3:

Changes in version 1.5.1:

Changes in version 1.5.0:

MSnbase

Changes in version 1.99.6:

Changes in version 1.99.5:

Changes in version 1.99.4:

Changes in version 1.99.3:

Changes in version 1.99.2:

Changes in version 1.99.1:

Changes in version 1.99.0:

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:

Changes in version 1.21.0:

MSnID

Changes in version 1.7.3:

Changes in version 1.7.2:

Changes in version 1.7.1:

msPurity

Changes in version 0.99.10:

Changes in version 0.99.9:

Changes in version 0.99.8:

Changes in version 0.99.4:

Changes in version 0.99.3:

Changes in version 0.99.2:

MSstats

Version: 3.5.5 Date: 2016-09-30 Text: BUG FIXES - dataProcess with fractionation sample when filling incomplete rows. Especially, not balanced fractionation for heavy and light, (heavy in one fractionation, no heavy in other fractionation) - groupComparison function : fix the issue with different columns from different summary Methods. - MaxQtoMSstats function : option removeMpeptides=FALSE are now available. (Thanks, Danielle) - In case of multiple injections per sample (from fractionation or multiple injections with different range of m/x), normalization is performed separately and multiple injections are merged in each sample. NEW FEATURES - Add ‘originalRUN’ column in xx$ProcessedData after dataProcess function. - Profile plot from dataProcessPlot distinguish censored missing data or not with different symbol. SIGNIFICANT CHANGES FOR METHOD - applied the algorithm for deciding the threshold of censoring. - Method for calculation of the LOB/LOD is changed. LOQ is not calculated anymore. Please check help files for details. - summaryMethod=’logOfSum’ option in dataProcess is retired. - modelBasedQCPlots work with output from groupComparison in order to check the normality assumption of linear mixed effect model for whole plot level inference.

Version: 3.5.1 Text: Fix bug : summaryMethod=‘logOfSum’, redesign for result table.

multiClust

Changes in version 6-19-16:

Changes in version 3-2-16:

Changes in version 2-13-16:

Changes in version 2-11-16:

MultiDataSet

Version: 1.2.0 Category: o Add wrappers for two functions to integrate omic data: mcia (from omicade4 package) and iClusterPlus Text:

Version: 1.2.0 Category: o Add advanced subsetting by phenotype and feature Text:

Version: 1.2.0 Category: BUG FIXES Text:

Version: 1.2.0 Category: o Solve subsetting issues when sampleNames is different from ID column. Text:

mzR

Changes in version 2.7.13:

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 2.7.1:

netprioR

Changes in version 0.99.1:

normr

Changes in version 0.99.6:

FEATURES

PERFORMANCE

Changes in version 0.99.5:

FEATURES

BUGFIXES

Changes in version 0.99.4:

BUGFIXES

Changes in version 0.99.3:

BUGFIXES

Changes in version 0.99.2:

FEATURES

BUGFIXES

Changes in version 0.99.1:

FEATURES

BUGFIXES

Changes in version 0.99.0:

FEATURES

OncoScore

Changes in version 1.1.2 (2016-09-28):

OncoSimulR

Changes in version 2.4.0:

Changes in version 2.3.17 (2017-09-22):

Changes in version 2.3.16 (2017-09-19):

Changes in version 2.3.15 (2017-09-14):

Changes in version 2.3.14 (2017-08-26):

Changes in version 2.3.13 (2017-08-19):

Changes in version 2.3.12 (2017-08-10):

Changes in version 2.3.11 (2017-08-10):

Changes in version 2.3.10 (2017-07-14):

Changes in version 2.3.9 (2017-07-09):

Changes in version 2.3.8 (2017-07-08):

Changes in version 2.3.7 (2016-07-05):

Changes in version 2.3.6 (2016-06-25):

Changes in version 2.3.5 (2016-06-25):

Changes in version 2.3.4 (2016-06-24):

Changes in version 2.3.3 (2016-06-23):

oppar

Changes in version 1.2.0:

BUG FIXES

OrganismDbi

Changes in version 1.16.0:

NEW FEATURES

MODIFICATIONS

PAA

Changes in version 1.7.1 (2016-05-13):

GENERAL

NEW FEATURES

IMPROVEMENTS

MODIFICATIONS

BUG FIXES

PanVizGenerator

Changes in version 1.1.3:

PathoStat

Changes in version 1.0.0:

pathVar

Version: 1.3.1 Date: 2016-10-13 Category: Updated pathVar to remove any warnings for Bioconductor release Text:

Pbase

Changes in version 0.13.3:

Changes in version 0.13.0:

pbcmc

Changes in version 1.1.1:

CODE

DOCUMENTATION

Changes in version 1.1.0:

VERSION

pcaExplorer

Changes in version 1.99.0:

OTHER NOTES

Changes in version 1.1.5:

NEW FEATURES

BUG FIXES

OTHER NOTES

Changes in version 1.1.3:

BUG FIXES

PGA

Changes in version 1.3.15:

Changes in version 1.3.10:

Changes in version 1.3.6:

Changes in version 1.3.5:

philr

Changes in version 0.99.0:

USER-VISIBLE CHANGES

Changes in version 0.3.0:

INTERNAL CHANGES

Changes in version 0.1.4:

USER-VISIBLE CHANGES

INTERNAL

Changes in version 0.1.3:

USER-VISIBLE CHANGES

Changes in version 0.1.0:

USER-VISIBLE CHANGES

Pi

Changes in version 0.99.5:

NEW FEATURES

piano

Changes in version 1.14:

NEW FEATURES

IMPROVEMENTS [credits to Alexey Sergushichev

BUG FIXES

Pigengene

Changes in version 0.99.25 (2016-10-02):

Changes in existing functions

Changes in version 0.99.8 (2016-05-18):

General

podkat

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:

polyester

Version: 1.99.3 Text: NB function now exported

Version: 1.99.3 Text: note that version 1.99.3 on GitHub was version 1.1.0 on Bioconductor.

Version: 1.99.2 Text: bug fix in fragment generation (last 2 bases of transcript were never sequenced)

Version: 1.99.1 Text:

procoil

Changes in version 2.1.3:

Changes in version 2.1.2:

Changes in version 2.1.1:

Changes in version 2.1.0:

pRoloc

Changes in version 1.13.16:

Changes in version 1.13.15:

Changes in version 1.13.14:

Changes in version 1.13.13:

Changes in version 1.13.12:

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Changes in version 1.13.7:

Changes in version 1.13.6:

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Changes in version 1.13.4:

Changes in version 1.13.3:

Changes in version 1.13.2:

Changes in version 1.13.1:

Changes in version 1.13.0:

pRolocGUI

Changes in version 1.7.5:

Changes in version 1.7.4:

Changes in version 1.7.3:

Prostar

Version: 1.5.13 Category: NEW FEATURES Text: In this version, the methods for missing values impuation from the package imp4p have been disabled because they are still under development. They will be available later.

Version: 1.5.11 Category: NEW FEATURES Text: When the user wants to convert a text file into a MSnset dataset, the options are available only when a file has been loaded.

Version: 1.5.9 Category: NEW FEATURES Text: This version is compliant with the version 1.5.9 of DAPAR

Version: 1.5.7 Category: NEW FEATURES Text: The R commands of all the operations made with prostar are available in the logSession tab. This allows the user to create a script to automatize the analysis of a dataset.

Version: 1.5.5 Category: NEW FEATURES Text: Prostar integrates the imp4p package for the imputation of missing values, w.r.t MNAR / MCAR

Version: 1.5.5 Category: NEW FEATURES Text: In the export tool, the user can select the columns of metadata he wants to keep

Version: 1.5.3 Category: NEW FEATURES Text: Prostar handles the format xlsx for Excel files

Version: 1.5.1 Category: NEW FEATURES Text: Add modules

Version: 1.5.1 Category: BUG FIXES Text:

ProteomicsAnnotationHubData

Changes in version 1.3.3:

proteoQC

Changes in version 1.9.4:

ProtGenerics

Changes in version 1.5.1:

Changes in version 1.5.0:

PureCN

Changes in version 1.2.0:

Focus on PureCN 1.2 was to dramatically improve user-friendliness

OTHER MAJOR ENHANCEMENTS

API CHANGES

OTHER NEW FEATURES

PLANNED FEATURES FOR PURECN 1.4 (BIOCONDUCTOR 3.5

pwOmics

Changes in version 3.1.1:

qcmetrics

Changes in version 1.11.3:

qpgraph

Changes in version 2.80:

USER VISIBLE CHANGES

Changes in version 2.60:

USER VISIBLE CHANGES

Changes in version 2.40:

BUG FIXES

Changes in version 2.20:

USER VISIBLE CHANGES

BUG FIXES

qsea

Changes in version 0.99.6:

Bugfixes

Changes in version 0.99.5:

New features

Bugfixes

Changes in version 0.99.4:

New functions

Bugfixes

Changes in version 0.99.3:

Bugfixes

Changes in version 0.99.2:

New functions

Bugfixes

Documentation

Changes in version 0.99.1:

Bugfixes

Changes in version 0.99.0:

QUBIC

Changes in version 1.0.3:

rBiopaxParser

Changes in version 2.12:

RCyjs

Changes in version 1.9.8:

BUG FIXES

Changes in version 1.8.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

ReactomePA

Changes in version 1.17.4:

Changes in version 1.17.3:

Changes in version 1.17.2:

Changes in version 1.17.1:

readat

Version: 0.99.0 Text:

recount

Changes in version 0.99.30:

NEW FEATURES

Changes in version 0.99.29:

BUF FIXES

Changes in version 0.99.0:

NEW FEATURES

regionReport

Changes in version 1.7.10:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.7.2:

SIGNIFICANT USER-VISIBLE CHANGES

regsplice

Version: 1.0.0 Text:

ReportingTools

Changes in version 2015-3-27:

Changes in version 2013-4-1:

RGraph2js

Changes in version 1.0.1:

Improvement

rGREAT

Changes in version 1.5.3:

rhdf5

Changes in version 2.18.0:

NEW FEATURES

USER VISIBLE CHANGES

RnBeads

Changes in version 1.5.1:

roar

Changes in version 1.9.1:

rols

Changes in version 2.1.3:

ropls

Changes in version 1.5.22:

INTERNAL MODIFICATION

Changes in version 1.5.20:

BUG CORRECTION

Changes in version 1.5.18:

INTERNAL MODIFICATION

Changes in version 1.5.16:

INTERNAL MODIFICATION

Changes in version 1.5.14:

NEW FEATURE

Changes in version 1.5.12:

INTERNAL MODIFICATION

Changes in version 1.5.10:

INTERNAL MODIFICATION

Changes in version 1.5.8:

INTERNAL MODIFICATION

Changes in version 1.5.6:

NEW FEATURE

Changes in version 1.5.4:

NEW FEATURE

Changes in version 1.5.2:

BUG FIXED

Changes in version 1.5.0:

NEW FEATURES

rpx

Changes in version 1.9.4:

Changes in version 1.9.3:

Rsamtools

Changes in version 1.25:

NEW FEATURES

BUG FIXES

rSFFreader

Version: 0.99.0 Category: Seattle time Text:

Version: 0.99.0 Category: Marc will contact you off-tracker for the follow-up Text:

Version: 0.99.0 Category: MS: If the version is set to 0.5, the package still goes to the release branch, or stays in devel Text:

Version: 0.99.0 Category: If it goes to release, I’m cool with that, it is still under construction, but functional Text:

Rsubread

Version: 1.24.0 Category: NEW FEATURES Text:

Version: 1.24.0 Category: o New parameters in featureCounts() function: fracOverlap' and tmpDir Text:

Version: 1.24.0 Category: o FeatureCounts can now perfrom fractional counting for both multi-mapping reads and multi-overlapping reads via its `fraction’ parameter Text:

Version: 1.24.0 Category: o Depreciate `PE_orientation’ parameter in featureCounts Text:

Version: 1.24.0 Category: o In-built annotation for hg38(GRCh38) is added to the package Text:

Version: 1.24.0 Category: o Improved reporting of mapping quality score (MQS) for align() and subjunc() functions Text:

Version: 1.24.0 Category: o Improved efficiency of exactSNP() function when calling SNPs from data with very high sequencing depth Text:

Version: 1.24.0 Category: o Improved documentation and screen output Text:

RTCA

Changes in version 2009-07-13:

RUVSeq

Changes in version 1.7:

S4Vectors

Changes in version 0.12.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DOCUMENTATION IMPROVEMENTS

DEPRECATED AND DEFUNCT

BUG FIXES

SC3

Changes in version 1.1.7:

Changes in version 1.1.6:

Changes in version 1.1.5:

scater

Changes in version 1.1.26:

scran

Changes in version 1.1.10:

SeqArray

Changes in version 1.14.0:

Changes in version 1.12.0-1.12.9:

SeqVarTools

Changes in version 1.11.3:

Changes in version 1.11.1:

SGSeq

Changes in version 1.8.0:

signeR

Changes in version 1.0.0:

Changes in version 0.99.17:

sincell

Changes in version 1.5.3:

SNPhood

Changes in version 1.3.4:

BUG FIXES

SNPRelate

Changes in version 1.8.0:

Changes in version 1.6.0-1.6.6:

specL

Changes in version 1.7.4 (2016-05-19):

Changes in version 1.7.1 (2016-05-13):

SummarizedExperiment

Version: 1.4.0 Category: NEW FEATURES Text: Add makeSummarizedExperimentFromDataFrame() function.

Version: 1.4.0 Category: NEW FEATURES Text: Add “acbind” and “arbind” methods for Matrix objects.

Version: 1.4.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Speed up “cbind” method for SummarizedExperiment objects based on a suggestion by Peter Hickey.

Version: 1.4.0 Category: DEPRECATED AND DEFUNCT Text: Remove exptData() getter and setter (were defunct in BioC 3.3).

Version: 1.4.0 Category: BUG FIXES Text:

SWATH2stats

Changes in version 1.3.10:

BUG FIXES

Changes in version 1.3.9:

NEW FEATURES

Changes in version 1.3.8:

BUG FIXES

Changes in version 1.3.7:

BUG FIXES

Changes in version 1.3.6:

NEW FEATURES

DOCUMENTATION

Changes in version 1.3.5:

NEW FEATURES

Changes in version 1.3.4:

NEW FEATURES

BUG FIXES

DOCUMENTATION

Changes in version 1.3.3:

BUG FIXES

Changes in version 1.3.0:

NEW FEATURES

Changes in version 1.2.3:

BUG FIXES

TarSeqQC

Changes in version 1.3.13:

CODE

Changes in version 1.3.12:

CODE

Changes in version 1.3.1:

CODE

Changes in version 2.2.0:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

TEQC

Changes in version 3.13.2:

Changes in version 3.13.1:

TFBSTools

Changes in version 3.4:

BUG FIXES

NEW FEATURES

Changes in version 3.3:

BUG FIXES

tofsims

Version: 099.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: changed function behvaiour in the whole package from call-by-ref to call-by value. Adjusted accordingly all examples and the vignette.

Version: 099.1 Category: INTERNALS Text: depends now on ProtGenerics from which it uses ‘mz’

Version: 099.1 Category: INTERNALS Text: exchanged various print() with message()

Version: 099.1 Category: BUGFIXES Text:

TPP

Version: 2.3.1 Category: Update version number after the new Bioconductor Release 3.3 was launched on Text:

Version: 2.3.1 Category: https://www.bioconductor.org/packages/release/bioc/html/TPP.html Text:

Version: 2.3.1 Category: The version number stays in accordance with Devel version in the new Release Text:

Version: 2.3.2 Category: Removed unit test that causes R CMD check to crash since the latest update of package ‘testthat Text:

Version: 2.3.3 Text: Bugfixes in the functions responsible for filtering by user-specified QC columns (e.g. ‘qssm’) for normalization set creation. It is now possible to leave the ‘otherRequirements’ slot in the normalization criteria empty.

Version: 2.3.3 Text: Fixed typos in function documentation of ‘analyzeTPPTR()’

Version: 2.3.3 Text: Fixed bug in plotColors for the case when no comparisons are specified

Version: 2.3.4 Text: Improved documentation of non-exported functions by ensuring that there is at least a one-line comment explaining what the function does.

Version: 2.99.0 Text: Major update: Extended package to analyse 2D-TPP experiments

Version: 2.99.0 Text: Major update: Extended package to analyse TPP-TR experiments by “non-parametric analysis of response curves” (NPARC), a non-parametrc spline-based test for treatment effects.

Version: 2.99.0 Text: Bugfix in ‘tpptrCurveFit’: restrict file names to 255 characters when creating melting curve plots in order to prevent file system crashes.

Version: 2.99.0 Text: New packages dependencies: dplyr, margrittr

Version: 2.99.0 Text: Bugfix in CCR workflow: avoid division by 0 when transforming foldchanges before dose-response curve fitting.

Version: 2.99.1 Text: Remove the complex reference data object from the data folder. Will be re- introduced lalter in a leaner format.

Version: 2.99.2 Text: Reduce data by “xz” compression

Version: 2.99.3-5 Text: Adapt notation of function names and input arguments for consistency with 1D (TPP-TR and TPP-CCR) part.

trackViewer

Changes in version 1.9.14:

Changes in version 1.9.13:

Changes in version 1.9.12:

Changes in version 1.9.11:

Changes in version 1.9.10:

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:

TRONCO

Changes in version 2.4.3:

Changes in version 2.4.2:

Changes in version 2.4.1:

TVTB

Changes in version 0.99.8 (2016-10-12):

Minor changes

Changes in version 0.99.7 (2016-10-12):

Minor changes

Changes in version 0.99.6 (2016-10-12):

Experimental changes

Changes in version 0.99.5 (2016-10-12):

Bug fix

Changes in version 0.99.4 (2016-10-12):

Experimental changes

Changes in version 0.99.3 (2016-10-12):

Experimental changes

Changes in version 0.99.2 (2016-10-11):

Bug fixes

Changes in version 0.99.1 (2016-10-10):

Major changes

Minor changes

Changes in version 0.99.0 (2015-09-15):

New features

Uniquorn

Changes in version 1.0.8 (2016-06-17):

Optimization confidence score

Changes in version 1.0.7 (2016-06-13):

Optimization confidence score

Changes in version 1.0.6 (2016-06-05):

Optimization of default confidence score

Changes in version 1.0.5 (2016-05-30):

Minor Bugfixes

Changes in version 1.0.4 (2016-05-27):

Introduction of confidence score

Changes in version 1.0.3 (2016-05-18):

Changes to treshold calculation

Changes in version 1.0.1 (2016-05-09):

Minor update of BED files

uSORT

Changes in version 0.99.4 (2016-10-12):

MODIFICATION

Changes in version 0.99.2 (2016-09-13):

MODIFICATION

Changes in version 0.99.1:

MODIFICATION

Changes in version 0.99.0 (2016-08-22):

MODIFICATION

variancePartition

Changes in version 1.3.11:

Changes in version 1.3.10:

Changes in version 1.3.8:

Changes in version 1.3.7:

Changes in version 1.3.6:

Changes in version 1.3.5:

Changes in version 1.3.4:

Changes in version 1.3.3:

VariantAnnotation

Changes in version 1.20.0:

NEW FEATURES

MODIFICATIONS

BUG FIXES

VariantFiltering

Changes in version 1.10:

USER VISIBLE CHANGES

wavClusteR

Changes in version 2.7.0:

xcms

Changes in version 1.49.7:

BUG FIXES

Changes in version 1.49.6:

USER VISIBLE CHANGES

Changes in version 1.49.5:

USER VISIBLE CHANGES

Changes in version 1.49.4:

BUG FIXES

Changes in version 1.49.3:

NEW FEATURE

USER VISIBLE CHANGES

BUG FIXES

OTHER CHANGES

Changes in version 1.49.2:

NEW FEATURE

Changes in version 1.49.1:

NEW FEATURE

xps

Changes in version 3.2:

VERSION xps-1.29.1

YAPSA

Changes in version 0.99.0:

Deprecated and Defunct Packages

1 software package (betr) was marked as deprecated, to be removed in the next release.

16 previously deprecated software packages were removed from the release.