May 1, 2018

Bioconductors:

We are pleased to announce Bioconductor 3.7, consisting of 1560 software packages, 342 experiment data packages, 919 annotation packages, and 21 workflows.

There are 98 new software packages, 16 new data experiment packages, 2 new workflows, and many updates and improvements to existing packages; Bioconductor 3.7 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 3.7

To update to or install Bioconductor 3.7:

  1. Install R >=3.5.0. Bioconductor 3.7 has been designed expressly for this version of R.

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

New Software Packages

There are 98 new software packages in this release of Bioconductor.

New Data Experiment Packages

There are 16 new data experiment packages in this release of Bioconductor.

New Workflows

NEWS from new and existing Software Packages

ABSSeq

Version: 2017-12-18 Date: 2017-12-18 Category: Updating! Refine qtotal (R funtion: qtotalNormalized Text:

Version: 2017-07-18 Date: 2017-07-18 Category: Updating! Adapt aFold model for complex design with linear model (R funtion: ABSSeqlm Text:

Version: 2017-06-02 Date: 2017-06-02 Text: 1) Updating! Introduce a new approach for normalization as qtotal (R funtion: qtotalNormalized) 2) aFold now moderates fold changes upon overall dispersion and gene-specific dispersion

Version: 2017-02-14 Date: 2017-02-14 Category: Updating! Adding new method: aFold to call DE via fold-change Text:

ADaCGH2

Changes in version 2.19.2 (2018-04-19):

Changes in version 2.19.1 (2018-04-17):

adaptest

Changes in version 1.0.0:

affycoretools

Version: 1.52.0 Category: Changed plotting for makeImages to use ggplot2 rather than lattice

Version: 1.52.0 Category: Added a new function, vennInLine, intended to allow for placement of

Version: 1.52.0 Category: Venn diagrams in Rmarkdown-derived HTML documents, particularly those

Version: 1.52.0 Category: that use the BiocStyle package for formatting. The Venn diagrams

Version: 1.52.0 Category: contain clickable links that will open HTML tables containing results

Version: 1.52.0 Category: for the genes that are found within that cell of the diagram

ALDEx2

Changes in version 1.10.1:

amplican

Changes in version 1.1.2:

AneuFinder

Changes in version 1.7.2:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

AnnotationFilter

Changes in version 1.3.1:

NEW FEATURES

AnnotationHub

Changes in version 2.12.0:

BUG FIXES

MODIFICATIONS

AnnotationHubData

Changes in version 1.10.0:

MODIFICATIONS

annotatr

Changes in version 1.6.0:

NEW FEATURES

USER-FACING CHANGES

BUGFIXES

anota2seq

Changes in version 1.0.1:

aroma.light

Changes in version 3.9.1 (2017-12-19):

NEW FEATURES

Changes in version 3.9.0 (2017-10-30):

ASICS

Version: 0.99.0 Category: First version submitted to Bioconductor Text:

Version: 0.99.0 Category: New features Text: preprocessing functions: baseline correction, alignment,

Version: 0.99.0 Category: normalisation Text: library of pure spectra management functions

Version: 0.99.0 Category: normalisation Text: binning algorithm

Version: 0.99.0 Category: normalisation Text: diagnosis tool to assess the quality of the quantification

Version: 0.99.0 Category: normalisation Text: post-quantification statistical analysis functions: PCA, OPLS-DA

Version: 0.99.0 Category: and Kruskal-Wallis test Text:

Version: 0.99.0 Category: Improvements Text: user’s guide

Version: 0.99.0 Category: Improvements Text: spectra quantification

Version: 0.99.0 Category: Improvements Text: parallel with BiocParallel package

Version: 0.99.0 Category: PREVIOUS VERSIONS ON CRAN Text:

Version: 0.99.0 Category: New features Text: data importation from Bruker files

Version: 0.99.0 Category: New features Text: spectra quantification

Version: 0.99.0 Category: New features Text: user’s guide

ASpli

Changes in version 1.5.1:

BUG FIXES

attract

Version: 1.31.1 Date: 2018-03-28 Category: Fix bug when custom gene set and expression set both have same type of gene IDs

AUCell

Changes in version 1.2.0:

BASiCS

Changes in version 1.1.63 (2018-04-27):

Changes in version 1.1.62 (2018-04-21):

Changes in version 1.1.61:

Changes in version 1.1.60 (2018-04-19):

Changes in version 1.1.59 (2018-04-19):

Changes in version 1.1.58 (2018-04-19):

Changes in version 1.1.57 (2018-04-16):

Changes in version 1.1.56 (2018-04-16):

Changes in version 1.1.55 (2018-04-16):

Changes in version 1.1.54 (2018-04-15):

Changes in version 1.1.53 (2018-04-13):

Changes in version 1.1.52 (2018-04-09):

Changes in version 1.1.51 (2018-03-26):

Changes in version 1.1.50 (2018-03-26):

Changes in version 1.1.49 (2018-03-22):

Changes in version 1.1.48 (2018-03-22):

Changes in version 1.1.47 (2018-03-21):

Changes in version 1.1.46 (2018-03-21):

Changes in version 1.1.45 (2018-03-21):

Changes in version 1.1.44 (2018-03-21):

Changes in version 1.1.43 (2018-03-20):

Changes in version 1.1.42 (2018-03-20):

Changes in version 1.1.41 (2018-03-20):

Changes in version 1.1.40 (2018-03-20):

Changes in version 1.1.39 (2018-03-20):

Changes in version 1.1.38 (2018-03-20):

Changes in version 1.1.37 (2018-03-20):

Changes in version 1.1.36 (2018-03-18):

Changes in version 1.1.35 (2018-03-18):

Changes in version 1.1.34 (2018-01-31):

Changes in version 1.1.33 (2018-01-30):

Changes in version 1.1.32 (2018-01-29):

Changes in version 1.1.31 (2018-01-22):

Changes in version 1.1.30 (2018-01-22):

Changes in version 1.1.29 (2017-12-21):

Changes in version 1.1.28 (2017-12-20):

Changes in version 1.1.27 (2017-12-20):

Changes in version 1.1.26 (2017-12-20):

Changes in version 1.1.24 (2017-12-18):

Changes in version 1.1.23 (2017-12-18):

Changes in version 1.1.22 (2017-12-15):

Changes in version 1.1.21 (2017-12-13):

Changes in version 1.1.20 (2017-12-11):

Changes in version 1.1.19 (2017-12-09):

Changes in version 1.1.18 (2017-12-08):

Changes in version 1.1.17 (2017-12-07):

Changes in version 1.1.16 (2017-11-29):

Changes in version 1.1.15 (2017-11-29):

Changes in version 1.1.14 (2017-11-29):

Changes in version 1.1.13 (2017-11-28):

Changes in version 1.1.12 (2017-11-28):

Changes in version 1.1.11 (2017-11-24):

Changes in version 1.1.10 (2017-11-27):

Changes in version 1.1.9 (2017-11-24):

Changes in version 1.1.8 (2017-11-21):

Changes in version 1.1.7 (2017-11-20):

Changes in version 1.1.6 (2017-11-15):

Changes in version 1.1.5 (2017-11-15):

Changes in version 1.1.4 (2017-11-12):

Changes in version 1.1.3 (2017-11-08):

Changes in version 1.1.2 (2017-11-08):

Changes in version 1.1.1 (2017-11-08):

Changes in version 1.1.0 (2017-08-16):

bcSeq

Version: 1.0.1 Category: fixed a bug for windows version that caused by pthread Text:

Version: 1.0.2 Category: added helper functions to preprocess user files Text: “trimRead” to trim adpators. “uniqueBar” to extract unique barcode sequence from the library file

Version: 1.0.3 Category: change “alignment” to “mapping” in the title Text:

Version: 1.0.4 Category: change “for” to “in” in the title Text:

beachmat

Changes in version 1.1.13:

bioCancer

Version: 1.7.05 Text: omit importFrom clusterProfiler plot

Version: 1.7.04 Text: export Diagrammer and viNetwork to report

Version: 1.7.04 Text: reset image size of circomics to 1024px

Version: 1.7.03 Text: Save network widgets as HTML and png

Version: 1.7.03 Text: use swithc buttom for Networking Tab.

Version: 1.7.03 Text: setwd(~)/ for windows system by setwd(Sys.getenv(“R_USER”))

Version: 1.7.02 Text: resolve conflicts renderMetabologram and renderCoffeewheel. redefine initCoffeewhell in /htmlwidges

Version: 1.7.02 Text: report circomics widget to markdown document

Version: 1.7.02 Text: Save static wheel as html and png (low resolution)

Version: 1.7.02 Text: need phantomJS to catupe html widget output as png file

Version: 1.7.01 Text: add helps to ? menu

Version: 1.7.01 Text: change stop message

Version: 1.7.01 Text: addResourcePath for figures

Version: 1.7.00 Category: metamorphosis: bioCancer is a radiant.data extension Text:

Version: 1.7.00 Category: reduce size of package by half 14 -> 7 mb Text:

BiocCheck

Changes in version 1.16:

BUG FIXES

BiocFileCache

Changes in version 1.3:

NEW FEATURES

SCHEMA CHANGE

USER-VISIBLE CHANGES

BUG CORRECTION

BiocInstaller

Changes in version 1.30.0:

NEW FEATURES

BiocParallel

Changes in version 1.14:

BUG FIXES

BiocStyle

Changes in version 2.8.0:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

biomaRt

Changes in version 2.36.0:

BUG FIXES

MINOR CHANGES

biosigner

Changes in version 1.7.4:

INTERNAL MODIFICATIONS

Changes in version 1.7.2:

INTERNAL MODIFICATIONS

biotmle

Changes in version 1.4.0:

bnbc

Changes in version 1.1.2:

BPRMeth

Changes in version 1.6.0:

BrowserViz

Changes in version 2.1.0:

NEW FEATURES

CAGEfightR

Changes in version 0.99:

CAGEr

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:

BACKWARDS-INCOMPATIBLE CHANGES

NEW FEATURES

OTHER CHANGES

DOCUMENTATION UPDATES

canceR

Version: 1.11.01 Text: rm gamma = 1.5 argument for grDevices::rainbow function

Version: 3.1 Text:

Version: 3.2 Text: dimensions levels will be plot. 1- dialogMetOption(): add “Circos” argument to make the difference between getMetDataMultipleGene() and getListMetData() 2- getGeneList(): add rm(“GeneListMSigDB””, envir=”myGlobalEnv”)

Cardinal

Changes in version 1.11.2:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.11.1 (2017-10-25):

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

cbaf

Changes in version 1.2.0 (2018-04-26):

New Features

ccfindR

Changes in version 0.99.4 (2018-04-06):

Changes

CellNOptR

Changes in version 1.25.0 (2018-01-10):

ChemmineR

Changes in version 2.32.0:

NEW FEATURES

chimeraviz

Changes in version 1.5.6:

CHANGES

Changes in version 1.5.1:

NEW FEATURES

ChIPanalyser

Changes in version 3.6:

paramters

chipenrich

Changes in version 2.4.0:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

IMPROVEMENTS

BUG FIXES

ChIPexoQual

Version: 1.3.1 Text:

Version: 1.3.2 Text:

ChIPpeakAnno

Changes in version 3.13.19:

Changes in version 3.13.18:

Changes in version 3.13.17:

Changes in version 3.13.16:

Changes in version 3.13.14:

Changes in version 3.13.12:

Changes in version 3.13.11:

Changes in version 3.13.10:

Changes in version 3.13.9:

Changes in version 3.13.8:

Changes in version 3.13.6:

Changes in version 3.13.5:

Changes in version 3.13.4:

Changes in version 3.13.3:

Changes in version 3.13.2:

Changes in version 3.13.1:

ChIPseeker

Changes in version 1.15.2:

Changes in version 1.15.1:

chromstaR

Changes in version 1.5.1:

SIGNIFICANT USER-LEVEL CHANGES

ClassifyR

Changes in version 2.0.0:

clusterExperiment

Changes in version 1.99.4 (2018-04-19):

Changes:

Changes in version 1.99.3 (2018-04-17):

Changes

Bugs

Changes in version 1.99.2 (2018-03-22):

Bugs

Changes in version 1.99.0 (2018-02-15):

Changes

Bugs

ClusterSignificance

Changes in version 1.7.3:

Changes in version 1.7.2:

Changes in version 1.7.1:

CNEr

Changes in version 3.5:

NEW FEATURES

CNVPanelizer

Changes in version 1.11.0:

coMET

Changes in version 1.11.5 (2018-04-11):

Changes in version 1.11.4 (2018-03-28):

Changes in version 1.11.3 (2018-02-25):

Changes in version 1.11.1 (2017-07-27):

ComplexHeatmap

Changes in version 1.17.1:

CountClust

Changes in version 1.6.1:

Changes in version 1.5.1:

CrispRVariants

Changes in version 1.7.12:

Changes in version 1.7.10:

Changes in version 1.7.9:

Changes in version 1.7.7:

Changes in version 1.7.5:

Changes in version 1.7.4:

Changes in version 1.7.2:

Changes in version 1.7.1:

csaw

Changes in version 1.13.1:

cydar

Changes in version 1.3.1:

cytofkit

Changes in version 1.11.3 (2018-01-19):

MODIFICATIONS

BUG FIXES

Changes in version 1.11.2 (2017-12-15):

MODIFICATIONS TO EXPRESSION LEVEL SCATTERPLOT

BUG FIXES

Changes in version 1.11.1 (2017-11-06):

MODIFICATIONS

BUG FIXES

dada2

Changes in version 1.7.8:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.7.7:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.7.6:

NEW FEATURES

Changes in version 1.7.5:

NEW FEATURES

Changes in version 1.7.4:

NEW FEATURES

Changes in version 1.7.3:

BUG FIXES

Changes in version 1.7.2:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.7.1:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.17.2:

Changes in version 1.17.1:

DaMiRseq

Changes in version 1.3.7:

DAPAR

Changes in version 1.11.15:

ddPCRclust

Version: 0.99.0 Text:

debrowser

Changes in version 1.6.6:

decontam

Changes in version 0.20.0:

NEW FEATURES

DeepBlueR

Version: 1.4.1 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

DEFormats

Changes in version 1.8.0:

SIGNIFICANT USER-VISIBLE CHANGES

DEGreport

Version: 1.15.4 Text: 2017-03-27 Lorena Pantano lorena.pantano@gmail.com Fix: Fix typo in variable inside degClean Fix: Remove all columsn with NA values in degClean Feature: Plot only when degPatterns has only one gene. Thanks Amir Jassim. Feature: Add geom_cor to plot correlation values to a ggplot2 plot. Feature: Add eachStep option to degPattern to apply groupDifference to each time point and not only to the maximum and minimum values. Feature: Add covariates dendograme to degCovariates. Fix: Wrong matrix in degPattern. Thanks Amir Jassim. Feature: Add option to filter genes in degPattern. Thanks Amir Jassim. Feature: Return raw and summarise table in degPattern Feature: Migrate to rmarkdown for vignette Feature: Return prcomp output when using degPCA Fix: Typo in degPattern function, and set up to FALSE the use of consensusCluster. Fix: degPlot to be able to work with one gene. Feature: Add the option to look for specific patterns, or genes as reference. Feature: Return scaled values if scale==TRUE in degPattern. Feature: Add values used in plots for degPattern function. Thanks to Amir Jassim. Feature: Get significants for a list of DEGSet objects binding the tables first, calculating a new FDR, and aplying the filter as last step. https://support.bioconductor.org/p/104059/#104072

Version: 1.15.2 Text: 2017-01-08 Lorena Pantano lorena.pantano@gmail.com Feature: Add support to list for significant and recover full table. Feature: Add support to different shrinkage estimator. Fix: Volcano plot was plotting wrong the shadows in the y-axis. Fix: Use correct option in DESeq2::results to count UP/DOWN genes. Feature: Allow to ask for up/down genes. Thanks to Radhika Khetani.

Version: 1.15.1 Text: 2017-11-13 Lorena Pantano lorena.pantano@gmail.com Fix: Add checking point in degPCA Feature: Add function to plot basic expression signatures.

DEP

Changes in version 1.1.5:

derfinder

Changes in version 1.13.8:

BUG FIXES

Changes in version 1.13.1:

NEW FEATURES

derfinderPlot

Changes in version 1.13.5:

BUG FIXES

Changes in version 1.13.4:

BUG FIXES

DESeq2

Changes in version 1.20.0:

DEsingle

Changes in version 0.99.12:

Changes in version 0.99.9:

Changes in version 0.99.0:

DiffBind

Changes in version 2.8.0:

diffcoexp

Changes in version 0.99.2:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 0.99.1:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 0.99.0:

SIGNIFICANT USER-VISIBLE CHANGES

diffcyt

Version: 1.0.0 Text:

diffHic

Changes in version 1.11.8:

diffuStats

Changes in version 1.0.0:

DMRcaller

Version: 1.11.1 Text: Added functions detect DMRs from biological replicates (beta regression) Added functions to compute/plot spatial correlation of methylation level Added function to extract GC content (useful for NOME-seq)

dmrseq

Changes in version 0.99.11 (2018-04-05):

Changes in version 0.99.8 (2018-03-21):

Changes in version 0.99.6 (2018-03-02):

DominoEffect

Changes in version 0.99.5:

NEW FEATURES

Changes in version 0.99.4:

NEW FEATURES

Changes in version 0.99.3:

NEW FEATURES

Changes in version 0.99.2:

NEW FEATURES

Changes in version 0.99.1:

NEW FEATURES

Changes in version 0.99.0:

NEW FEATURES

DOSE

Changes in version 3.5.2:

drawProteins

Version: 0.99.10 Category: ARGUEMENT Text: show.legend added as argument to allow the option to show or not show the legend as per ggplot2.

Version: 0.99.9 Category: FEATURES Text: New function called draw_recept_dom(). This function allows the drawing of the TOPO_DOM and TRANSMEM types of receptors. Data from TNFR1 and CD40 are included to demonstate the function.

Version: 0.99.8 Category: FEATURES Text: New function called extact_transcripts. This function will ammend the data frame to allow each chain from the same UniProt accession number to to drawn separately. A vignette entitled drawProteins_extract_transcripts has been written to demonstrate.

Version: 0.99.8 Category: FEATURES Text: LazyData is now false and NAMESPACE updated as per Bioconductor review.

Version: 0.98.3 Category: FEATURES Text: New function called draw_canvas. This function was previously within draw_chains but has now been pulled out to allow the generation of a canvas separately from the chains. It did require quite a rewrite but I think it will make things more useful For example, it will allow the plotting of domains without chains which has the potential to be very useful.

Version: 0.98.2 Category: FEATURES Text: Rename functions from geom to draw. E.g geom_chains is now geom_draw. This is because they weren’t really geoms and using the word draw seem more helpful and a better reflection of the function.

Version: 0.98.2 Category: LAUNCH VERSION 0.98.1 Text:

Version: 0.98.2 Category: FEATURES Text: Drawing protein schematics from Uniprot database with Accession numbers

DropletUtils

Changes in version 0.99.0:

easyRNASeq

Changes in version 2.15.5:

Changes in version 2.15.4:

EBImage

Changes in version 4.22.0:

BUG FIXES

edgeR

Changes in version 3.22.0:

EGSEA

Changes in version 1.6.1 (2017-12-03):

EnrichedHeatmap

Changes in version 1.9.3:

Changes in version 1.9.2:

EnrichmentBrowser

Changes in version 2.10.0:

ensembldb

Changes in version 2.3.14:

Changes in version 2.3.11:

Changes in version 2.3.9:

Changes in version 2.3.8:

Changes in version 2.3.7:

Changes in version 2.3.6:

BUG FIXES

Changes in version 2.3.5:

BUG FIXES

Changes in version 2.3.2:

NEW FEATURES

Changes in version 2.3.1:

NEW FEATURES

ensemblVEP

Changes in version 1.22.0:

NEW FEATURES

MODIFICATIONS

epiNEM

Version: 2017.01 Category: Github made public and submitted to Bioconductor Text:

epivizrData

Changes in version 999.999:

epivizrServer

Changes in version 999.999:

epivizrStandalone

Changes in version 999.999:

erccdashboard

Changes in version 1.13.1:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES AND MINOR IMPROVEMENTS

esATAC

Version: 1.2.0 Category: Publication Text:

Version: 1.2.0 Category: Wei, Zheng, et al. “esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis.” Bioinformatics (2018 Text:

Version: 1.2.0 Category: https://doi.org/10.1093/bioinformatics/bty141 Text:

Version: 1.2.0 Category: Fix some known bugs Text:

Version: 1.2.0 Category: Speed up motif scanning Text:

Version: 2018.04.18 Category: Using the new method to scan motif in the genome, remove preset motif data. The new method Text:

Version: 2018.04.18 Category: is from package “motifmatchr”, it cost less than 2mins for a sample(test sample: SRR891268; Text:

Version: 2018.04.18 Category: of course, depend on your computer performance Text:

FamAgg

Changes in version 1.7.4:

Changes in version 1.7.3:

fCCAC

Changes in version 1.5.1:

FELLA

Version: 0.99.6 Text: Small corrections in vignette

Version: 0.99.6 Text: Removed rm calls

Version: 0.99.5 Text: Small correction in vignette

Version: 0.99.5 Text: Version bump to see if bioc build is bugged

Version: 0.99.4 Text: Moved contents of NEWS.md to NEWS

Version: 0.99.4 Text: Deleted most of data-raw folder, moved the rest to inst/script

Version: 0.99.4 Text: Removed redundant Authors field in DESCRIPTION

Version: 0.99.4 Text: Removed class(data) != "FELLA.DATA" by using built-in is.FELLA.DATA

Version: 0.99.3 Text: Version bump (biomaRt down?)

Version: 0.99.2 Text: Fixed more doc links

Version: 0.99.1 Text: Fixed doc links (hopefully)

Version: 0.99.1 Text: Updated funding in vignette

Version: 0.99.1 Text: Travis will only test the devel branch

Version: 0.99.0 Text: Submission to Bioconductor

fgsea

Changes in version 1.5.2:

Changes in version 1.5.1:

flowcatchR

Changes in version 1.14.0:

NEW FEATURES

OTHER NOTES

flowPloidy

Changes in version 1.5.6 (2018-03-08):

User Visible Changes

Internal Changes

Changes in version 1.5.3 (2018-01-17):

User Visible Changes

Changes in version 1.5.1 (2017-12-04):

Minor bug squashed

gage

Changes in version 2.28.2:

GARS

Changes in version 0.99.0:

GDSArray

Changes in version 0.99.11:

Changes in version 0.99.10:

Changes in version 0.99.7:

Changes in version 0.99.6:

Changes in version 0.99.5:

Changes in version 0.99.1:

gdsfmt

Changes in version 1.16.0:

UTILITIES

BUG FIXES

Changes in version 1.14.0-1.14.1:

UTILITIES

GeneNetworkBuilder

Changes in version 1.21.2:

Changes in version 1.21.1:

GENESIS

Changes in version 2.9.3:

GeneStructureTools

Version: 0.99.0 Category: Pre-BioC submission Text:

Version: 0.99.1 Category: Fixes for BioC submission Text: notNMD is not required for vignettes

Version: 0.99.1 Category: Fixes for BioC submission Text: whippet files are read in as a single object

Version: 0.99.1 Category: Fixes for BioC submission Text: Fixed bug where leafcutter set creation snowballed

Version: 0.99.2 Text: Fix for fread()’ing in gzip files on windows

Version: 0.99.4 Text: Exon skipping and intron retention now works with manual coordinates again

Version: 0.99.4 Text: Documentation updates

genomation

Version: 1.11.3 Category: IMPROVEMENTS AND BUG FIXES Text: fixed an error of data.table() function that occurs when GrangesList object contains unnamed windows

Version: 1.11.3 Category: in ScoreMatrixBin() function Text:

Version: 1.11.2 Category: IMPROVEMENTS AND BUG FIXES Text: improved the C++ function Median_c() to handle NAs

Version: 1.11.2 Category: IMPROVEMENTS AND BUG FIXES Text: the following C++ functions return NAs instead of zeros if the length of the vector is smaller than the number of bins: binMean(), binMedian(), binMax(), binMin(), binSum()

Version: 1.11.2 Category: NEW FUNCTIONS AND FEATURES Text:

Version: 1.11.2 Category: C++ functions that compute a desired value from a vector and handle NAs Text: Mean_c() - computes a mean value,

Version: 1.11.2 Category: C++ functions that compute a desired value from a vector and handle NAs Text: Max_c() - computes a maximum values,

Version: 1.11.2 Category: C++ functions that compute a desired value from a vector and handle NAs Text: Min_c() - computes a minumum values,

Version: 1.11.2 Category: C++ functions that compute a desired value from a vector and handle NAs Text: Sum_c() - computes a sum value.

Version: 1.11.1 Category: IMPROVEMENTS AND BUG FIXES Text: bug fix relating to ScorematrixBin that returns all 1’s when is.noCovNA=T (https://github.com/BIMSBbioinfo/genomation/issues/168)

Version: 1.11.1 Category: IMPROVEMENTS AND BUG FIXES Text: xcoords argument for heatMatrix and multiHeatMatrix now can take character vectors.

Version: 1.11.1 Category: The character vectors will label the x-axis of heatmaps. Examples: xcoords=c(“-2kb”,”0”,”2kb Text:

GenomicAlignments

Changes in version 1.16.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

GenomicFeatures

Changes in version 1.32.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

GenomicRanges

Changes in version 1.32.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

GenomicScores

Changes in version 1.4.0:

USER VISIBLE CHANGES

genphen

Changes in version 1.7 (2018-01-20):

Introduction

Changes

To do

GEOquery

Version: 2.47.1 Text: Bug fixes: * Fixes problems with intermittent connection issues (which were not intermittend connection problems, it seems)

ggtree

Changes in version 1.11.3:

Changes in version 1.11.2:

Changes in version 1.11.1:

GOfuncR

Changes in version 0.99.14:

NEW FEATURES

Changes in version 0.99.12:

USER-LEVEL CHANGES

GOpro

Version: 1.5.1 Text:

graphite

Changes in version 1.25.9 (2018-04-28):

Changes in version 1.25.7 (2018-04-18):

Changes in version 1.25.6 (2018-04-11):

Changes in version 1.25.3 (2018-03-23):

Changes in version 1.25.2 (2018-03-23):

Changes in version 1.25.1 (2017-12-13):

GreyListChIP

Changes in version 1.11.1:

GSVA

Changes in version 1.28:

USER VISIBLE CHANGES

HDTD

Changes in version 1.13.3 (2018-01-10):

Changes in version 1.13.2 (2017-12-10):

Changes in version 1.13.1 (2017-11-20):

HIBAG

Changes in version 1.16.0:

hipathia

Changes in version 0.99.27 (2018-04-08):

Changes in version 0.99.9 (2018-03-09):

Changes in version 0.99.8 (2018-03-07):

Changes in version 0.99.7 (2018-02-14):

HiTC

Changes in version 1.23.0:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

hpar

Changes in version 1.21.1:

HTSFilter

Version: 1.19.3 Category: —- Fixed bug for the DESeqDataSet class when there are additional columns in the Text:

Version: 1.19.3 Category: colData of the object beyond those used in the design (thanks to Stephanie Durand Text:

Version: 1.19.3 Category: for finding the bug!) Text: – Keep rownames and colnames on filtered data for matrix and data.frame class

ideal

Changes in version 1.4.0:

NEW FEATURES

BUG FIXES

OTHER NOTES

InPAS

Changes in version 1.11.4:

Changes in version 1.11.3:

Changes in version 1.11.2:

InTAD

Changes in version 0.99.1-4:

IntEREst

Changes in version 1.4.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

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:

IRanges

Changes in version 2.14.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

iSEE

Changes in version 0.99.3:

Changes in version 0.99.2:

Changes in version 0.99.1:

Changes in version 0.99.0:

JASPAR2018

Changes in version 3.6:

NEW FEATURES

kissDE

Changes in version 0.99.0:

Logolas

Changes in version 1.3.1:

Changes in version 1.2.1:

maftools

Changes in version 1.6.00:

NEW FUNCTIONS

SIGNIFICANT USER-LEVEL IMPROVEMENT

MAGeCKFlute

Changes in version 0.99.19:

Changes in version 0.99.18:

Changes in version 0.99.10:

Changes in version 0.99.1:

Changes in version 0.99.0:

matter

Changes in version 1.5.4:

NEW FEATURES

Changes in version 1.5.3:

NEW FEATURES

BUG FIXES

Changes in version 1.5.2 (2017-11-12):

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.5.1:

NEW FEATURES

mCSEA

Changes in version 0.99.0:

metagenomeFeatures

Changes in version 1.99.9 (2018-04-02):

metagenomeSeq

Changes in version 1.21:

MetaGxOvarian

Changes in version 0.99.0:

NEW FEATURES

metaMS

Changes in version 1.15.1:

metaseqR

Changes in version 1.19.14 (2018-04-12):

NEW FEATURES

BUG FIXES

metavizr

Changes in version 1.3.20:

Changes in version 1.3.11:

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 1.3.6:

Changes in version 1.3.5:

Changes in version 1.3.4:

MetCirc

Changes in version 1.9.1:

Changes in version 1.7.0:

methimpute

Changes in version 1.1.1:

NEW FEATURES

methylKit

Changes in version 1.5.3:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.5.2:

IMPROVEMENTS AND BUG FIXES

methyvim

Changes in version 1.1.0:

minfi

Changes in version 1.25:

miRNAmeConverter

Changes in version 1.7.2:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

DEPRECATED AND DEFUNCT

miRsponge

Version: 1.5.2 Category: Update ground truth for validation <2018-04-17, Tues Text:

Version: 1.5.1 Category: Update netModule and spongeValidate function <2018-04-16, Mon Text:

Version: 1.5.0 Category: Update Reference Manual <2018-04-15, Sun Text:

Version: 1.3.3 Category: Update netModule function <2018-04-12, Thur Text:

Version: 1.3.2 Category: Update DESCRIPTION <2018-03-07, Wed Text:

Version: 1.3.1 Category: Update Reference Manual <2018-03-03, Sat Text:

Version: 1.3.0 Category: Update Reference Manual <2018-02-28, Wed Text:

MLInterfaces

Changes in version 1.59.2:

Changes in version 1.59.1:

monocle

Changes in version 2.6.1:

motifcounter

Changes in version 1.3.2:

motifStack

Changes in version 1.23.12:

Changes in version 1.23.11:

Changes in version 1.23.10:

Changes in version 1.23.9:

Changes in version 1.23.8:

Changes in version 1.23.7:

Changes in version 1.23.6:

Changes in version 1.23.5:

Changes in version 1.23.4:

Changes in version 1.23.3:

Changes in version 1.23.2:

Changes in version 1.23.1:

msa

Changes in version 1.12.0:

Changes in version 1.11.2:

Changes in version 1.11.1:

Changes in version 1.11.0:

MSnbase

Changes in version 2.5.14:

Changes in version 2.5.13:

Changes in version 2.5.12:

Changes in version 2.5.11:

Changes in version 2.5.10:

Changes in version 2.5.9:

Changes in version 2.5.8:

Changes in version 2.5.7:

Changes in version 2.5.6:

Changes in version 2.5.5:

Changes in version 2.5.4:

Changes in version 2.5.3:

Changes in version 2.5.2:

Changes in version 2.5.1:

Changes in version 2.5.0:

msPurity

Changes in version 1.5.1:

Changes in version 1.4.1:

MSstats

Version: 3.11.6 Date: 2018-04-23 Text: BUG FIXES - SkylinetoMSstatsFormat : fix the inconsistency of column name from Skyline output

Version: 3.11.5 Date: 2018-02-22 Text: BUG FIXES - add the package, stringr, for DIAUmpiretoMSstatsFormat function

Version: 3.11.4 Date: 2018-02-19 Text: BUG FIXES - add set.seed for sample size calculation of classification

Version: 3.11.3 Date: 2018-02-15 Text: BUG FIXES - nonlinear_quantlim : fix the bug for the resampling of the blank sample, increase the default number of bootstrap samples - designSampleSize : fix the bug NEW FEATURES - new function : designSampleSizeClassification, designSampleSizeClassificationPlots - Calculate the optimal size of training data for classification problem by simulation. - new converter functions : DIAUmpiretoMSstatsFormat, OpenMStoMSstatsFormat

Version: 3.10.5 Date: 2018-01-10 Text: BUG FIXES - SpectronauttoMSstatsFormat : TRUE or FALSE are allowed for the values of the column, F.ExcludedFromQuantification. Check the value for this column.

Version: 3.10.4 Date: 2017-12-22 Text: BUG FIXES - MaxQtoMSstatsFormat : ‘fewmeasurements’ bug fixed

Version: 3.10.2 Date: 2071-11-27 Text: BUG FIXES - make error messages for QQ plot and residual plot, if the protein couldn’t be fitted by linear mixed effect model. - ProgenesistoMSstatsFormat : make more generalization for different format.

multiClust

Changes in version 11-14-17:

MutationalPatterns

Version: 3.6 Category: MutationalPatterns v1.3.2 (Release date: 2017-10-24 Text:

Version: 3.6 Category: Bugfixes Text: Removed deprecated functions from previous release.

Version: 3.6 Category: Bugfixes Text: Improved examples in documentation.

Version: 3.6 Category: MutationalPatterns v1.3.1 (Release date: 2017-10-24 Text:

Version: 3.6 Category: Bugfixes Text: Fix running of the code examples.

Version: 3.6 Category: MutationalPatterns v1.3.0 (Release date: 2017-10-22 Text:

Version: 3.6 Category: Bugfixes Text: To determine the transcriptional strand of mutations in genes, all mutations that overlap with multiple genes were excluded. When these genes are on different strands, it can indeed not be determined whether a mutation is on the transcribed or untransribed strand. However, if these overlapping genes are all on the same strand, the transcriptional strand can be determined, but these were unneccesarily removed from the analysis. This bug is now fixed, and as a result more mutations are now included in the analysis. This bugfix influences the results of: ‘mut_strand’ (previously ‘strand_from_vcf’) and ‘mut_matrix_stranded’

Version: 3.6 Category: Renamed functions Text: ‘strand_from_vcf’ to ‘mut_strand’

Version: 3.6 Category: Renamed functions Text: ‘mutation_types’ to ‘mut_type’

Version: 3.6 Category: Renamed functions Text: ‘mutation_context’ to ‘mut_context’

Version: 3.6 Category: New features & parameter changes Text: Replicative strand bias analyses - ‘mut_strand’ and ‘mut_matrix_stranded’ can now be executed in two modes: ‘transcription’ (default) or ‘replication’ - All downstream analyses can be performed for both modes with ‘strand_occurrences’, ‘strand_bias_test’ and ‘plot_strand_bias’

Version: 3.6 Category: New features & parameter changes Text: Condensed plotting option for ‘plot_96_profile’ and ‘plot_192_profile’ condensed = F (default), or condensed = T

Version: 3.6 Category: New functions Text: ‘plot_contribution_heatmap’: to visualize the relative contribution of mutational signatures in a heatmap. Samples can be hierarchically clustered.

Version: 3.6 Category: New functions Text: ‘cos_sim’: to calculate the cosine similarity between two vectors.

Version: 3.6 Category: New functions Text: ‘cos_sim_matrix’: to calculate all pairwise similarities between mutational profiles

Version: 3.6 Category: New functions Text: ‘cluster_signatures’: to hierarchically cluster signatures based on cosine similarity

Version: 3.6 Category: New functions Text: ‘plot_cosine_heatmap’: to visualize pairwise cosine similarities between mutational profiles in a heatmap Sample can be hierarchically clustered.

Version: 3.6 Category: MutationalPatterns v1.1.3 (Release date: 2017-04-20 Text:

Version: 3.6 Category: Fourth preparation release for Bioconductor 3.5 Text:

Version: 3.6 Category: Bugfixes Text: Add missing package to ‘Suggest’ field.

Version: 3.6 Category: MutationalPatterns v1.1.3 (Release date: 2017-04-20 Text:

Version: 3.6 Category: Third preparation release for Bioconductor 3.5 Text:

Version: 3.6 Category: Bugfixes Text: Fix running of a unit test.

Version: 3.6 Category: Bugfixes Text: Fix another build problem for Windows.

Version: 3.6 Category: MutationalPatterns v1.1.2 (Release date: 2017-04-18 Text:

Version: 3.6 Category: Third preparation release for Bioconductor 3.5 Text:

Version: 3.6 Category: Bugfixes Text: Properly read external data for tests.

Version: 3.6 Category: Bugfixes Text: Fix build problems on Windows.

Version: 3.6 Category: MutationalPatterns v1.1.1 (Release date: 2017-04-12 Text:

Version: 3.6 Category: Second preparation release for Bioconductor 3.5 Text:

Version: 3.6 Category: MutationalPatterns v1.1.0 (Release date: 2017-04-06 Text:

Version: 3.6 Category: Preparations for Bioconductor release 3.5 Text:

Version: 3.6 Category: Interface changes Text: ‘read_vcfs_as_granges’: The ‘genome’ parameter must now be the name of a BSgenome library, to prevent problems with seqlevels style. The function now accepts an optional ‘group’ parameter to use a subset of chromosomes. It also accepts the new optional ‘check_alleles’ parameter to significantly speed up the reading of VCF files.

Version: 3.6 Category: Interface changes Text: ‘plot_contribution’: This function now accepts an optional parameter ‘palette’ to specify custom colors.

Version: 3.6 Category: Performance updates Text: Implement parallel execution in ‘read_vcfs_as_granges’, ‘mut_matrix’ and ‘mut_matrix_stranded’.

Version: 3.6 Category: Bugfixes Text: Fix ‘mut_type_occurences’ to handle missing types.

Version: 3.6 Category: Bugfixes Text: Fix ‘mut_matrix’ and ‘mut_matrix_stranded’ to emit warnings when processing empty GRanges.

Version: 3.6 Category: Bugfixes Text: Fix inconsistencies in the README and the vignette.

Version: 3.6 Category: Other changes Text: Various vignette updates.

Version: 3.6 Category: Other changes Text: Added unit tests for ‘read_vcfs_as_granges’, ‘mut_matrix’, and ‘mut_matrix_stranded’.

Version: 3.6 Category: MutationalPatterns v1.0.0 (Release date: 2016-10-19 Text:

Version: 3.6 Category: Bioconductor release 3.4 Text:

Version: 3.6 Category: MutationalPatterns v0.99.6 (Release date: 2016-10-14 Text:

Version: 3.6 Category: Changes Text: Renamed functions: ‘mut_type_occurences’ to ‘mut_type_occurrences’, ‘strand_occurences’ to ‘strand_occurrences’.

Version: 3.6 Category: MutationalPatterns v0.99.5 (Release date: 2016-10-06 Text:

Version: 3.6 Category: Changes Text: Added deprecation and defunct messages to functions that have changed since the v0.99.0.

Version: 3.6 Category: Changes Text: Various small vignette and reference manual updates.

Version: 3.6 Category: MutationalPatterns v0.99.4 (Release date: 2016-10-05 Text:

Version: 3.6 Category: Changes Text: Internal package loading changes.

Version: 3.6 Category: Changes Text: Removed files that do not belong to the package.

Version: 3.6 Category: MutationalPatterns v0.99.3 (Release date: 2016-09-28 Text:

Version: 3.6 Category: Changes Text: Renamed functions: ‘get_mut_context’ to ‘mutation_context’, ‘get_type_context’ to ‘type_context’, ‘get_muts’ to ‘mutations_from_vcf’, ‘get_strand’ to ‘strand_from_vcf’.

Version: 3.6 Category: Changes Text: Added an explanation for the difference between SomaticSignatures and MutationalPatterns in the vignette.

Version: 3.6 Category: MutationalPatterns v0.99.2 (Release date: 2016-09-23 Text:

Version: 3.6 Category: Changes Text: Renamed functions: ‘vcf_to_granges’ to ‘read_vcfs_as_granges’, ‘get_types’ to ‘mutation_types’.

Version: 3.6 Category: MutationalPatterns v0.99.1 (Release date: 2016-09-13 Text:

Version: 3.6 Category: Changes Text: Renamed functions: ‘read_vcf’ to ‘vcf_to_granges’.

Version: 3.6 Category: Changes Text: Removed functions: ‘bed_to_granges’, ‘estimate_rank’, ‘rename_chrom’.

Version: 3.6 Category: Changes Text: Parameter changes: ‘plot_rainfall’, ‘vcf_to_granges’

Version: 3.6 Category: MutationalPatterns v0.99.0 (Release date: 2016-09-12 Text:

Version: 3.6 Category: Changes Text: Package created

mzR

Changes in version 2.13.8:

Changes in version 2.13.7:

Changes in version 2.13.6:

Changes in version 2.13.5:

Changes in version 2.13.4:

Changes in version 2.13.3:

Changes in version 2.13.2:

Changes in version 2.13.1:

ndexr

Changes in version 1.1.7:

Changes in version 1.1.2:

NOISeq

Changes in version 2.22.1 (2018-02-01):

OmaDB

Version: 0.99.9 Date: 2017-10-14 Category: Initial release to Bioconductor Text:

omicplotR

Changes in version 0.99.4:

Changes in version 0.99.3:

Changes in version 0.99.0:

OncoSimulR

Changes in version 2.10.0:

Changes in version 2.9.10 (2018-04-19):

Changes in version 2.9.9 (2018-04-10):

Changes in version 2.9.8 (2018-03-26):

Changes in version 2.9.7 (2018-02-20):

Changes in version 2.9.6 (2017-12-27):

Changes in version 2.9.5:

Changes in version 2.9.4 (2017-11-30):

Changes in version 2.9.3 (2017-11-27):

Changes in version 2.9.2 (2017-11-24):

Changes in version 2.9.1 (2017-11-10):

ORFik

Changes in version 1.0.0:

PanVizGenerator

Changes in version 1.7.0:

PathoStat

Changes in version 1.8.1:

pathview

Changes in version 1.18.2:

pcaExplorer

Changes in version 2.6.0:

NEW FEATURES

BUG FIXES

OTHER NOTES

PGA

Changes in version 1.9.1:

phantasus

Changes in version 0.99.34:

Changes in version 0.99.28:

Changes in version 0.99.24:

Changes in version 0.99.23:

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 0.99.18:

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:

piano

Version: 1.20.0 Category: none yet Text:

Version: 1.18.1 Category: BUG FIXES Text: Fix parsing of gmt files when gene-set name contains spaces

Pigengene

Changes in version 1.5.22 (2018-04-28):

Bug Fixes

Changes in version 1.5.9 (2018-03-12):

General

Changes in existing functions

Changes in version 1.5.6 (2018-01-19):

Changes in existing functions

Changes in version 1.5.2 (2017-11-10):

New functions

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:

PowerExplorer

Changes in version 0.99.0:

powerTCR

Version: 0.1.1 Category: Getting compliant with BioConductor policies Text:

Version: 0.1.1 Category: INITIAL RELEASE Text:

pRoloc

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:

Prostar

Changes in version 1.11.13:

BUG FIXES

NEW FEATURES

Changes in version 1.11.4:

BUG FIXES

PureCN

Changes in version 1.10.0:

qcmetrics

Changes in version 1.17.1:

qpgraph

Changes in version 2.14:

USER VISIBLE CHANGES

BUG FIXES

RamiGO

Changes in version 1.26.0:

ramwas

Changes in version 1.3.0:

NEW FEATURES

BUG FIXES

rCGH

Changes in version 1.9.1:

Minor changes

RcisTarget

Changes in version 0.99.7:

Changes in version 0.99.6:

Changes in version 0.99.1:

Changes in version 0.7:

Changes in version 0.6:

RCy3

Version: 2.0 Category: For Developers Text: Reorganized functions into files corresponding to CyREST API, e.g., Collections, CytoscapeSystem, Layouts, Networks, etc. Normalized all documentation using roxygen2 Streamlined interfaces to CyREST and Commands API (see above), greatly facilitating the implementation of any new functions matching CyREST or Command API additions Reverted all single-instance methods to simple functions, replacing class-based signatures with simple default values Established handy functions for validating network and view SUIDs getNetworkName getNetworkSuid getNetworkViewSuid

Version: 2.0 Category: Deprecated Text: Outdated function names

Version: 2.0 Category: Defunct Text: CytoscapeConnection and CytoscapeWindow classes, functions and parameters

ReactomePA

Changes in version 1.23.2:

Changes in version 1.23.1:

recount

Changes in version 1.5.11:

BUG FIXES

Changes in version 1.5.9:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.5.6:

NEW FEATURES

Changes in version 1.5.5:

BUG FIXES

Changes in version 1.5.4:

BUG FIXES

Changes in version 1.5.3:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

recoup

Changes in version 1.7.2 (2018-04-25):

NEW FEATURES

BUG FIXES

RedeR

Changes in version 1.28.0:

rGREAT

Changes in version 1.11.1:

rgsepd

Changes in version 1.11.2:

BUG FIXES

rhdf5

Changes in version 2.24.0:

NEW FEATURES

BUG FIXES

Rhtslib

Changes in version 1.12.0:

SIGNIFICANT USER-VISIBLE CHANGES

RiboProfiling

Changes in version 1.7.2:

RnBeads

Changes in version 1.11.9:

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 1.11.4:

Changes in version 1.11.2:

roar

Changes in version 1.15.2:

rols

Changes in version 2.7.2:

Changes in version 2.7.1:

Changes in version 2.7.0:

RPA

Changes in version 1.35.2 (2017-11-12):

Rsamtools

Changes in version 1.31:

BUG FIXES

RSeqAn

Changes in version 0.99.0:

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: 1.30.0 Category: NEW FEATURES Text:

Version: 1.30.0 Category: o New parameters in featureCounts() to give more control on the size of overlap between read and feature - ‘nonOverlap’ and ‘nonOverlapFeature Text:

Version: 1.30.0 Category: o New parameter in featureCounts() to specify the path where files containing counting results for each read are saved - ‘reportReadsPath Text:

Version: 1.30.0 Category: o New parameter in align() and subjunc() to allow reads in the mapping output to have the same order as in the FASTQ file - ‘keepReadOrder Text:

Version: 1.30.0 Category: o Reduce running time in outputting BAM files in align() and subjunc() via saving data to disk with multi threads Text:

Version: 1.30.0 Category: o Annotation file (eg. GTF, SAF or VCF annotation) in featureCounts(), align(), subjunc() and exactSNP() can be provided as a gzipped file Text:

Version: 1.30.0 Category: o Tilda (‘~’) is allowed to be included in file names provided to functions. Text:

Version: 1.30.0 Category: o Improve running time of featureCounts for the processing of BAM files generated by some other aligners and the Picard tool Text:

RTN

Changes in version 2.4.0:

RTNduals

Changes in version 1.4.0:

rWikiPathways

Changes in version 1.0.0:

NEW FEATURES

SIGNIFICANT CHANGES UNDER THE HOOD

BUG FIXES

S4Vectors

Changes in version 0.18.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

sampleClassifier

Version: 22.11.2017 Text:

scater

Changes in version 1.7.18:

scDD

Changes in version 1.3.4 (2018-03-26):

Changes in version 1.3.3 (2018-03-23):

scmeth

Changes in version 0.99.38:

PKG FEATURES

scPipe

Changes in version 1.0.9:

Changes in version 1.0.8:

Changes in version 1.0.6 (2017-12-18):

Changes in version 1.0.5 (2017-12-14):

Changes in version 1.0.4 (2017-12-04):

Changes in version 1.0.3 (2017-12-03):

Changes in version 1.0.2 (2017-12-01):

Changes in version 1.0.1 (2017-11-28):

scran

Changes in version 1.7.28:

SDAMS

Version: 0.99.7 Category: package submission Text:

SeqArray

Changes in version 1.20.0:

UTILITIES

NEW FEATURES

Changes in version 1.18.1-1.18.2:

BUG FIXES

seqCAT

Changes in version 1.2.0:

FEATURES

FIXES

SeqVarTools

Changes in version 1.17.8:

Changes in version 1.17.7:

Changes in version 1.17.6:

Changes in version 1.17.2:

sevenC

Changes in version 0.99.0:

ShortRead

Changes in version 1.37:

BUG FIXES

signeR

Changes in version 1.5.2:

Changes in version 1.5.1:

SIMLR

Changes in version 1.5.1 (2018-03-09):

SingleCellExperiment

Changes in version 1.1.4:

singleCellTK

Changes in version 0.99.3:

Changes in version 0.6.3:

Changes in version 0.4.7:

Changes in version 0.4.5:

singscore

Changes in version 0.99.9:

Changes in version 0.99.8:

Changes in version 0.99.5:

Changes in version 0.99.3:

Changes in version 0.99.2:

SNPRelate

Changes in version 1.14.0:

Changes in version 1.12.2:

Changes in version 1.12.1:

SparseSignatures

Changes in version 1.0.0:

specL

Changes in version 1.13.02 (2017-11-20):

splatter

Changes in version 1.3.5 (2017-04-25):

SPONGE

Changes in version 1.0.3:

Changes in version 1.0.2:

Changes in version 1.0.1:

SummarizedExperiment

Changes in version 1.10.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

SWATH2stats

Changes in version 1.9.3:

BUG FIXES

Changes in version 1.9.2:

NEW FEATURES

Changes in version 1.9.1:

NEW FEATURES

Changes in version 1.8.1:

NEW FEATURES

synapter

Changes in version 2.3.1:

TargetSearch

Changes in version 1.36.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 2.7.13:

TEQC

Version: 4.0.1 Category: fixed problem with IRanges version >=2.13.28 in coverage.target Text:

Version: 4.0.0 Text: package is now based on ‘GRanges’ objects instead of deprecated ‘RangedData’ objects

Version: 4.0.0 Text: vignette is now created with knitr

TFBSTools

Changes in version 3.5:

NEW FEATURES

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:

ToPASeq

Changes in version 1.13.2:

topdownr

Changes in version 1.1.7:

Changes in version 1.1.6:

Changes in version 1.1.5:

Changes in version 1.1.4:

Changes in version 1.1.3:

Changes in version 1.1.2:

Changes in version 1.1.1:

Changes in version 1.1.0:

trackViewer

Changes in version 1.15.13:

Changes in version 1.15.12:

Changes in version 1.15.11:

Changes in version 1.15.10:

Changes in version 1.15.9:

Changes in version 1.15.8:

Changes in version 1.15.7:

Changes in version 1.15.6:

Changes in version 1.15.5:

Changes in version 1.15.4:

Changes in version 1.15.3:

Changes in version 1.15.2:

Changes in version 1.15.1:

transcriptogramer

Changes in version 1.1.18:

Changes in version 1.1.17:

Changes in version 1.1.7:

Changes in version 1.1.6:

Changes in version 1.1.3:

treeio

Changes in version 1.3.9:

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:

Changes in version 1.3.2:

Changes in version 1.3.1:

tRNAscanImport

Changes in version 0.99.21 (2018-03-17):

Changes

TVTB

Changes in version 1.5.4 (2017-09-24):

Bug fix

tximport

Changes in version 1.8.0:

TxRegInfra

Version: 0.99.10 Category: NEW FEATURES Text:

Uniquorn

Changes in version 1.99.3 (2018-01-03):

Bioconductor compliance

Changes in version 1.99.2 (2018-20-02):

Added RNA-seq and panel-seq capability

Changes in version 1.99.1 (2018-12-02):

Added RNA-seq and panel-seq capability

Changes in version 1.99.0 (2018-15-01):

Added RNA-seq and panel-seq capability

variancePartition

Changes in version 1.9.9:

Changes in version 1.9.8:

Changes in version 1.9.6:

Changes in version 1.9.2:

Changes in version 1.9.1:

VariantFiltering

Changes in version 1.16:

USER VISIBLE CHANGES

xcms

Changes in version 3.1.3:

BUG FIXES

Changes in version 3.1.2:

NEW FEATURES

BUG FIXES

Changes in version 3.1.1:

NEW FEATURES

BUG FIXES

xps

VERSION xps-1.37.2

VERSION xps-1.37.1

Changes in version 3.3:

zinbwave

Changes in version 1.1.6 (2018-04-17):

Changes in version 1.1.5 (2018-02-15):

NEWS from new and existing Data Experiment Packages

ASICSdata

Version: 0.99.2 Category: Fixed a few typos Text:

Version: 0.99.1 Category: Updated R version dependency from 3.4 to 3.5 Text:

Version: 0.99.0 Category: First submitted version to Bioconductor Text:

chipenrich.data

Changes in version 2.4.0:

dsQTL

Changes in version 2.17:

USER VISIBLE CHANGES

flowPloidyData

Changes in version 1.5.3 (2018-01-19):

User Visible Changes

HDCytoData

Version: 1.0.0 Text:

mCSEAdata

Changes in version 0.99.0:

MetaGxBreast

Changes in version 0.99.0:

NEW FEATURES

MetaGxOvarian

Changes in version 0.99.0:

NEW FEATURES

MetaGxPancreas

Changes in version 0.99.0:

NEW FEATURES

microRNAome

Changes in version 1.1.2:

mtbls2

Changes in version 1.9.1:

pRolocdata

Changes in version 1.17.4:

Changes in version 1.17.3:

Changes in version 1.17.2:

Changes in version 1.17.1:

PtH2O2lipids

Changes in version 2016-04-21:

RcisTarget.hg19.motifDBs.cisbpOnly.500bp

Changes in version 0.99.7:

RforProteomics

Changes in version 1.17.1:

Changes in version 1.17.0:

Changes in version 1.16.0:

TargetSearchData

Changes in version 1.17.2:

SIGNIFICANT USER-VISIBLE CHANGES

tissueTreg

Changes in version 0.99.3:

Changes in version 0.99.2:

Changes in version 0.99.1:

Changes in version 0.99.0:

topdownrdata

Changes in version 1.1.1:

Changes in version 1.1.0:

Deprecated and Defunct Packages

Nine software packages were removed from this release (after being deprecated in BioC 3.6): BioMedR, ddgraph, EWCE, HCsnip, stepwiseCM, domainsignatures, iontree, oneChannelGUI, RCytoscape. One software package was removed from Bioconductor at user request (mvGST) without previous deprecation.

Ten software packages (ontoCat, spliceR, GMRP, MBttest, OperaMate, DASC, htSeqTools, PAnnBuilder, phenoDist, BrowserVizDemo) are deprecated in this release and will be removed in BioC 3.8.

One annotation data package (IlluminaHumanMethylation450k.db) was removed from this release.

Three experimental data packages (RnaSeqTutorial, cheung2010, MEALData) are deprecated in this release and will be removed in Bioc 3.8.