October 14, 2015

Bioconductors:

We are pleased to announce Bioconductor 3.2, consisting of 1104 software packages, 257 experiment data packages, and 917 up-to-date annotation packages.

There are 80 new software packages, and many updates and improvements to existing packages; Bioconductor 3.2 is compatible with R 3.2, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release includes an updated Bioconductor Amazon Machine Image and Docker containers.

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

Contents

Getting Started with Bioconductor 3.2

To update to or install Bioconductor 3.2:

  1. Install R 3.2. Bioconductor 3.2 has been designed expressly for this version of R.

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

New Software Packages

There are 80 new packages in this release of Bioconductor.

ABAEnrichment - The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function ‘aba_enrich’ integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project. ‘aba_enrich’ interfaces the ontology enrichment software FUNC to perform the statistical analyses. Additional functions provided in this package like ‘get_expression’ and ‘plot_expression’ facilitate exploring the expression data.

acde - This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It uses artificial components, close to the data’s principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR). The methods on this package are described in the vignette or in the article ‘Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments’ by J. P. Acosta, L. Lopez-Kleine and S. Restrepo (2015, pending publication).

AnnotationHubData - These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.

BBCAnalyzer - BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.

biobroom - This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same the tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.

caOmicsV - caOmicsV package provides methods to visualize multi-dimentional cancer genomics data including of patient information, gene expressions, DNA methylations, DNA copy number variations, and SNP/mutations in matrix layout or network layout.

CausalR - Causal Reasoning algorithms for biological networks, including predictions, scoring, p-value calculation and ranking

ChIPComp - ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control.

CNPBayes - Bayesian hierarchical mixture models for batch effects and copy number.

CNVPanelizer - A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level.

DAPAR - This package contains a collection of functions for the visualisation and the statistical analysis of proteomic data.

DChIPRep - The DChIPRep package implements a methodology to assess differences between chromatin modification profiles in replicated ChIP-Seq studies as described in Chabbert et. al - http://www.dx.doi.org/10.15252/msb.20145776.

DeMAND - DEMAND predicts Drug MoA by interrogating a cell context specific regulatory network with a small number (N >= 6) of compound-induced gene expression signatures, to elucidate specific proteins whose interactions in the network is dysregulated by the compound.

destiny - Create and plot diffusion maps

DiffLogo - DiffLogo is an easy-to-use tool to visualize motif differences.

DNABarcodes - The package offers a function to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode.

dupRadar - Duplication rate quality control for RNA-Seq datasets.

ELMER - ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.

EnrichedHeatmap - Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement Enriched heatmap by ComplexHeatmap package. Since this type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources.

erma - Software and data to support epigenomic road map adventures.

eudysbiome - eudysbiome a package that permits to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases (as indicated in literature) or as unknown based on their ambiguous genus classification. Further, the package statistically measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition.

fCI - (f-divergence Cutoff Index), is to find DEGs in the transcriptomic & proteomic data, and identify DEGs by computing the difference between the distribution of fold-changes for the control-control and remaining (non-differential) case-control gene expression ratio data. fCI provides several advantages compared to existing methods.

FindMyFriends - A framework for doing microbial comparative genomics in R. The main purpose of the package is assisting in the creation of pangenome matrices where genes from related organisms are grouped by similarity, as well as the analysis of these data. FindMyFriends provides many novel approaches to doing pangenome analysis and supports a gene grouping algorithm that scales linearly, thus making the creation of huge pangenomes feasible.

gcatest - GCAT is an association test for genome wide association studies that controls for population structure under a general class of trait. models.

GeneBreak - Recurrent breakpoint gene detection on copy number aberration profiles.

genotypeeval - Takes in a gVCF or VCF and reports metrics to assess quality of calls.

GEOsearch - GEOsearch is an extendable search engine for NCBI GEO (Gene Expression Omnibus). Instead of directly searching the term, GEOsearch can find all the gene names contained in the search term and search all the alias of the gene names simultaneously in GEO database. GEOsearch also provides other functions such as summarizing common biology keywords in the search results.

GUIDEseq - The package implements GUIDE-seq analysis workflow including functions for obtaining unique cleavage events, estimating the locations of the cleavage sites, aka, peaks, merging estimated cleavage sites from plus and minus strand, and performing off target search of the extended regions around cleavage sites.

Guitar - The package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.

hierGWAS - Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers.

HilbertCurve - Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still keep the locality. This package aims to provide a easy and flexible way to visualize data through Hilbert curve.

iCheck - QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.

iGC - This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.

Imetagene - This package provide a graphical user interface to the metagene package. This will allow people with minimal R experience to easily complete metagene analysis.

INSPEcT - INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and asses via modeling the rates that determines changes in mature mRNA levels.

IONiseR - IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.

ldblock - Define data structures for linkage disequilibrium measures in populations.

LedPred - This package aims at creating a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, next-generation sequencing (NGS) peaks and signals and other numerical scores of the sequences using supervised classification. The package contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences, optimize SVM parameters and feature number and creates a model that can be stored and used to score the regulatory potential of unknown sequences.

lfa - LFA is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter.

LOLA - Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This make is possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data.

MEAL - Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several plotting functionalities are included as well as a new region analysis based on redundancy analysis. Effect of SNPs on a region can also be estimated.

metagenomeFeatures - metagenomeFeatures was developed for use in exploring the taxonomic annotations for a marker-gene metagenomic sequence dataset. The package can be used to explore the taxonomic composition of a marker-gene database or annotated sequences from a marker-gene metagenome experiment.

metaX - The package provides a integrated pipeline for mass spectrometry-based metabolomic data analysis. It includes the stages peak detection, data preprocessing, normalization, missing value imputation, univariate statistical analysis, multivariate statistical analysis such as PCA and PLS-DA, metabolite identification, pathway analysis, power analysis, feature selection and modeling, data quality assessment.

miRcomp - Based on a large miRNA dilution study, this package provides tools to read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves.

mirIntegrator - Tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.

miRLAB - Provide tools exploring miRNA-mRNA relationships, including popular miRNA target prediction methods, ensemble methods that integrate individual methods, functions to get data from online resources, functions to validate the results, and functions to conduct enrichment analyses.

motifbreakR - We introduce motifbreakR, which allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. MotifbreakR is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum probability matrix, 2) log-probabilities, and 3) weighted by relative entropy. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor (currently there are 22).

myvariant - MyVariant.info is a comprehensive aggregation of variant annotation resources. myvariant is a wrapper for querying MyVariant.info services

NanoStringDiff - This Package utilizes a generalized linear model(GLM) of the negative binomial family to characterize count data and allows for multi-factor design. NanoStrongDiff incorporate size factors, calculated from positive controls and housekeeping controls, and background level, obtained from negative controls, in the model framework so that all the normalization information provided by NanoString nCounter Analyzer is fully utilized.

OGSA - OGSA provides a global estimate of pathway deregulation in cancer subtypes by integrating the estimates of significance for individual pathway members that have been identified by outlier analysis.

OperaMate - OperaMate is a flexible R package dealing with the data generated by PerkinElmer’s Opera High Content Screening System. The functions include the data importing, normalization and quality control, hit detection and function analysis.

Oscope - Oscope is a statistical pipeline developed to identifying and recovering the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. The Oscope pipeline includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.

Path2PPI - Package to predict pathway specific protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI uses PPIs of the pathway of interest from other well established model organisms to predict a certain pathway in the target organism. Path2PPI only depends on the sequence similarity of the involved proteins.

pathVar - This package contains the functions to find the pathways that have significantly different variability than a reference gene set. It also finds the categories from this pathway that are significant where each category is a cluster of genes. The genes are separated into clusters by their level of variability.

PGA - This package provides functions for construction of customized protein databases based on RNA-Seq data, database searching, post-processing and report generation. This kind of customized protein database includes both the reference database (such as Refseq or ENSEMBL) and the novel peptide sequences form RNA-Seq data.

Prize - The high throughput studies often produce large amounts of numerous genes and proteins of interest. While it is difficult to study and validate all of them. Analytic Hierarchy Process (AHP) offers a novel approach to narrowing down long lists of candidates by prioritizing them based on how well they meet the research goal. AHP is a mathematical technique for organizing and analyzing complex decisions where multiple criteria are involved. The technique structures problems into a hierarchy of elements, and helps to specify numerical weights representing the relative importance of each element. Numerical weight or priority derived from each element allows users to find alternatives that best suit their goal and their understanding of the problem.

Prostar - This package provides a GUI interface for DAPAR.

ProteomicsAnnotationHubData - These recipes convert a variety and a growing number of public proteomics data sets into easily-used standard Bioconductor data structures.

RareVariantVis - Genomic variants can be analyzed and visualized using many tools. Unfortunately, number of tools for global interrogation of variants is limited. Package RareVariantVis aims to present genomic variants (especially rare ones) in a global, per chromosome way. Visualization is performed in two ways - standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family data, for example in search for causative variants in rare Mendelian diseases.

rCGH - A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through Agilent and Affymetrix microarrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, and Affymetrix SNP6.0 and cytoScan probeset.txt, cychp.txt, and cnchp.txt files, exported from ChAS or Affymetrix Power Tools. This package takes over all the steps required for a genomic profile analysis, from reading the files to the segmentation and genes annotations, and provides several visualization functions (static or interactive) which facilitate profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.

RCy3 - Vizualize, analyze and explore graphs, connecting R to Cytoscape >= 3.2.1.

RiboProfiling - Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3’UTR, and 5’UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.

rnaseqcomp - Several quantitative and visualized benchmarks for RNA-seq quantification pipelines. Two-replicate quantifications for genes, transcripts, junctions or exons by each pipeline with nessasery meta information should be organizd into numeric matrix in order to proceed the evaluation.

ropls - Latent variable modeling with Principal Component Analysis (PCA) and Partial Least Squares (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. Orthogonal Partial Least Squares (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation. Successful applications of these chemometrics techniques include spectroscopic data such as Raman spectroscopy, nuclear magnetic resonance (NMR), mass spectrometry (MS) in metabolomics and proteomics, but also transcriptomics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients). The package can be accessed via a user interface on the Workflow4Metabolomics.org online resource for computational metabolomics (built upon the Galaxy environment).

RTCGA - The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients’ treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.

RTCGAToolbox - Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.

sbgr - R client for Seven Bridges Genomics API.

SEPA - Given single-cell RNA-seq data and true experiment time of cells or pseudo-time cell ordering, SEPA provides convenient functions for users to assign genes into different gene expression patterns such as constant, monotone increasing and increasing then decreasing. SEPA then performs GO enrichment analysis to analysis the functional roles of genes with same or similar patterns.

SICtools - This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.

SISPA - Sample Integrated Gene Set Analysis (SISPA) is a method designed to define sample groups with similar gene set enrichment profiles.

SNPhood - To date, thousands of single nucleotide polymorphisms (SNPs) have been found to be associated with complex traits and diseases. However, the vast majority of these disease-associated SNPs lie in the non-coding part of the genome, and are likely to affect regulatory elements, such as enhancers and promoters, rather than function of a protein. Thus, to understand the molecular mechanisms underlying genetic traits and diseases, it becomes increasingly important to study the effect of a SNP on nearby molecular traits such as chromatin environment or transcription factor (TF) binding. Towards this aim, we developed SNPhood, a user-friendly Bioconductor R package to investigate and visualize the local neighborhood of a set of SNPs of interest for NGS data such as chromatin marks or transcription factor binding sites from ChIP-Seq or RNA-Seq experiments. SNPhood comprises a set of easy-to-use functions to extract, normalize and summarize reads for a genomic region, perform various data quality checks, normalize read counts using additional input files, and to cluster and visualize the regions according to the binding pattern. The regions around each SNP can be binned in a user-defined fashion to allow for analysis of very broad patterns as well as a detailed investigation of specific binding shapes. Furthermore, SNPhood supports the integration with genotype information to investigate and visualize genotype-specific binding patterns. Finally, SNPhood can be employed for determining, investigating, and visualizing allele-specific binding patterns around the SNPs of interest.

subSeq - Subsampling of high throughput sequencing count data for use in experiment design and analysis.

SummarizedExperiment - The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.

SWATH2stats - This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.

synlet - Select hits from synthetic lethal RNAi screen data. For example, there are two identical celllines except one gene is knocked-down in one cellline. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA. Quality control and various visualisation tools are implemented. Four different algorithms could be used to pick up the interesting hits. This package is designed based on 384 wells plates, but may apply to other platforms with proper configuration.

TarSeqQC - The package allows the representation of targeted experiment in R. This is based on current packages and incorporates functions to do a quality control over this kind of experiments and a fast exploration of the sequenced regions. An xlsx file is generated as output.

TCGAbiolinks - The aim of TCGAbiolinks is : i) facilitate the TCGA open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) allow the user to download a specific version of the data and thus to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

traseR - traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.

variancePartition - Quantify and interpret multiple sources and biological and technical variation in gene expression experiments. Uses linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables.

XBSeq - We developed a novel algorithm, XBSeq, where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. The mapped reads in non-exonic regions are considered as sequencing noises, which follows a Poisson distribution. Given measureable observed and noise signals from RNA-seq data, true expression signals, assuming governed by the negative binomial distribution, can be delineated and thus the accurate detection of differential expressed genes.

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:

acde

Changes in version 0.99.0:

NEW FEATURES

ADaCGH2

Changes in version 2.9.3 (2015-05-30):

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affxparser

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AllelicImbalance

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annotate

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DEFUNCT

AnnotationDbi

Changes in version 1.31:

NEW FEATURES and API changes

AnnotationHub

Changes in version 2.1.26:

SIGNIFICANT USER-VISIBLE CHANGES

AnnotationHubData

Changes in version 1.0.0:

BUG FIXES

Changes in version 0.0.214:

NEW FEATURES

antiProfiles

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aroma.light

Changes in version 2.99.0 (2015-10-06):

ballgown

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BaseSpaceR

biobroom

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BiocInstaller

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BUG FIXES

BiocStyle

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biocViews

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BrowserViz

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bsseq

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CAMERA

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BUG FIXES

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USER VISIBLE CHANGES

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Cardinal

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BUG FIXES

ChIPpeakAnno

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FIX BUGS

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NEW FEATURE

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ChIPseeker

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ClassifyR

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cleanUpdTSeq

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clonotypeR

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clusterProfiler

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CNVPanelizer

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cogena

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compEpiTools

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ComplexHeatmap

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CopywriteR

Changes in version 2.0.6 (2015-06-15):

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COSNet

Changes in version 1.3.2:

csaw

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customProDB

Changes in version 1.8.2:

UPDATED FUNCTIONS

Changes in version 1.7.2:

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BUG FIXES

Changes in version 1.7.1:

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DART

Changes in version 1.17.1:

DChIPRep

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ddCt

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deepSNV

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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

1.4.0: 07-03-2015 Lorena Pantano lorena.pantano@gmail.com FIX SOME TEXT IN VIGNETTE, AND CLEAN DEPENDS FLAG

deltaGseg

Changes in version 1.9.0:

derfinder

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Changes in version 1.3.1:

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derfinderHelper

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derfinderPlot

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DESeq2

Changes in version 1.10.0:

DiffBind

Changes in version 1.16.0:

diffHic

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DOSE

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DSS

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dupRadar

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DOCUMENTATION

easyRNASeq

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EBImage

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EBSeq

Changes in version 1.9.3:

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EDASeq

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edge

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edgeR

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ENmix

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EnrichedHeatmap

Changes in version 0.99.3:

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ensembldb

Changes in version 1.1.9:

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Changes in version 1.1.1:

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ensemblVEP

Changes in version 1.10.0:

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epivizr

Changes in version 1.6.1:

erccdashboard

Changes in version 1.3.5:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES AND MINOR IMPROVEMENTS

Changes in version 1.3.4:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES AND MINOR IMPROVEMENTS

Changes in version 1.3.3:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES AND MINOR IMPROVEMENTS

Changes in version 1.3.2:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES AND MINOR IMPROVEMENTS

Changes in version 1.3.1:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES AND MINOR IMPROVEMENTS

exomePeak

Changes in version 1.9.2:

Changes in version 1.9.1:

FGNet

Changes in version 3.4:

FindMyFriends

Changes in version 0.99.0:

flipflop

Changes in version 1.7.3:

flowcatchR

Changes in version 1.4.0:

NEW FEATURES

BUG FIXES

OTHER NOTES

FlowRepositoryR

Changes in version 1.1.1:

NEW FEATURES

flowType

Changes in version 2.7.0:

gdsfmt

Changes in version 1.6.0:

GeneNetworkBuilder

Changes in version 1.11.1:

GENESIS

Changes in version 2.0.0:

geNetClassifier

Changes in version 1.9.3:

Changes in version 1.9:

genomation

Changes in version 1.1.27:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.26:

NEW FUNCTIONS AND FEATURES

Changes in version 1.1.25:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.24:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.23:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.22:

NEW FUNCTIONS AND FEATURES

Changes in version 1.1.21:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.20:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.19:

NEW FUNCTIONS AND FEATURES

Changes in version 1.1.18:

NEW FUNCTIONS AND FEATURES

Changes in version 1.1.17:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.16:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.15:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.14:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.13:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.12:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.11:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.10:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.9:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.8:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.7:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.6:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.5:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.4:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.3:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.2:

IMPROVEMENTS AND BUG FIXES

Changes in version 1.1.1:

NEW FUNCTIONS AND FEATURES

IMPROVEMENTS AND BUG FIXES

genomeIntervals

Changes in version 1.25.3:

Changes in version 1.25.2:

Changes in version 1.25.1:

Changes in version 1.25.0:

GenomicAlignments

Changes in version 1.6.0:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

GenomicFeatures

Changes in version 1.22:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

GenomicFiles

Changes in version 1.6.0:

BUG FIXES

GenomicInteractions

Changes in version 1.3.9:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

BUG FIXES

GenomicRanges

Changes in version 1.22.0:

NEW FEATURES

SIGNIFICANT USER-LEVEL CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

genotypeeval

Changes in version 0.99.0:

GEOquery

2.36: New Features * New, faster SOFT format parsing (Leonardo Gama) * Turned on unit tests in Travis CI * Test coverage metrics added Bug fixes * default download method no longer assumes that curl is installed on linux * GSEMatrix parsing from file now finds cached GPLs

ggtree

Changes in version 1.1.20:

Changes in version 1.1.19:

Changes in version 1.1.18:

Changes in version 1.1.17:

Changes in version 1.1.16:

Changes in version 1.1.15:

Changes in version 1.1.14:

Changes in version 1.1.13:

Changes in version 1.1.12:

Changes in version 1.1.11:

Changes in version 1.1.10:

Changes in version 1.1.9:

Changes in version 1.1.8:

Changes in version 1.1.7:

Changes in version 1.1.6:

Changes in version 1.1.5:

Changes in version 1.1.4:

Changes in version 1.1.3:

Changes in version 1.1.2:

Changes in version 1.1.1:

girafe

Changes in version 1.21.1:

GOexpress

Changes in version 1.3.2:

BUG FIX

Changes in version 1.3.1:

BUG FIX

GOSemSim

Changes in version 1.27.4:

Changes in version 1.27.3:

Changes in version 1.27.2:

Changes in version 1.27.1:

graphite

Changes in version 1.15.3 (2015-10-07):

GreyListChIP

Changes in version 1.1.1:

GSAR

Changes in version 1.4.0:

GSEABase

Changes in version 1.31:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

gtrellis

Changes in version 1.1.1:

Guitar

Changes in version 0.99.9:

gwascat

Changes in version 2.1.0:

USER VISIBLE CHANGES

GWASTools

Changes in version 1.15.16:

Changes in version 1.15.15:

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 1.15.8:

Changes in version 1.15.7:

Changes in version 1.15.5:

Changes in version 1.15.3:

Changes in version 1.15.2:

Changes in version 1.15.1:

HDTD

Changes in version 1.3.4 (2015-09-08):

Changes in version 1.3.3 (2015-07-20):

Changes in version 1.3.2 (2015-05-26):

Changes in version 1.3.1 (2015-05-12):

Heatplus

Changes in version 2.15.2:

hiAnnotator

Changes in version 1.3.2:

Changes in version 1.3.1:

HIBAG

Changes in version 1.6.0:

hierGWAS

Changes in version 0.99.3:

HilbertCurve

Changes in version 0.99.3:

Changes in version 0.99.2:

Changes in version 0.99.1:

Changes in version 0.99.0:

hiReadsProcessor

Changes in version 1.4.0:

HiTC

Changes in version 1.13.2:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Changes in version 1.13.1:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

hpar

Changes in version 1.11.1:

Changes in version 1.11.0:

iGC

Changes in version 1.0.0:

illuminaio

Changes in version 0.11.2 (2015-09-11):

Changes in version 0.11.1 (2015-07-29):

Changes in version 0.11.0 (2015-04-16):

immunoClust

1.1.1: NEW FEATRUES: * A normalization step which the sample cell-clusters to the common meta-cluster model is included an optionally activated during the major meta-clustering process. CHANGES: * The meta.ME C-binding and return value was modified in a way that the A-Posterior probability matrix Z for a cell-cluster belonging to a meta-cluster is also calculated and returned. BUFIXES: * Ellipse position were not correct when ploting a parameter subset

InPAS

Changes in version 1.1.9:

Changes in version 1.1.8:

BUG FIXES

Changes in version 1.1.7:

BUG FIXES

Changes in version 1.1.6:

BUG FIXES

Changes in version 1.1.5:

BUG FIXES

Changes in version 1.1.4:

BUG FIXES

Changes in version 1.1.3:

BUG FIXES

Changes in version 1.1.2:

BUG FIXES

Changes in version 1.1.1:

BUG FIXES

interactiveDisplayBase

Changes in version 1.7:

NEW FEATURES

BUG FIXES

IRanges

Changes in version 2.4.0:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

BUG FIXES

kebabs

Changes in version 1.3.4:

Changes in version 1.3.3:

Changes in version 1.3.2:

Changes in version 1.3.1:

Changes in version 1.3.0:

KEGGgraph

Changes in version 1.27.2 (2015-05-25):

Changes in version 1.27.1 (2015-05-04):

mAPKL

Changes in version 1.1.1:

metabomxtr

Changes in version 1.3.6:

Changes in version 1.3.1:

metagene

Changes in version 2.2.0:

metagenomeFeatures

Changes in version 0.0.0.9 (2015-09-14):

metagenomeSeq

Changes in version 1.11:

metaseqR

Changes in version 1.9.21 (2015-10-08):

NEW FEATURES

BUG FIXES

Changes in version 1.9.0 (2015-05-27):

NEW FEATURES

BUG FIXES

metaX

Changes in version 0.1.0:

methylPipe

Changes in version 1.3.3:

Changes in version 1.3.2:

minfi

Changes in version 1.15:

MLInterfaces

Changes in version 1.49.8:

Changes in version 1.49.7:

Changes in version 1.49.1:

mogsa

Changes in version 1.1.1:

NEW FEATURES

motifStack

Changes in version 1.13.8:

NEW FEATURES

Changes in version 1.13.7:

Changes in version 1.13.6:

BUG FIXES

Changes in version 1.13.5:

NEW FEATURES

Changes in version 1.13.4:

NEW FEATURES

BUG FIXES

Changes in version 1.13.3:

NEW FEATURES

BUG FIXES

Changes in version 1.13.2:

NEW FEATURES

BUG FIXES

Changes in version 1.13.1:

NEW FEATURES

BUG FIXES

msa

Changes in version 1.2.0:

MSnbase

Changes in version 1.17.16:

Changes in version 1.17.15:

Changes in version 1.17.14:

Changes in version 1.17.13:

Changes in version 1.17.12:

Changes in version 1.17.11:

Changes in version 1.17.10:

Changes in version 1.17.9:

Changes in version 1.17.8:

Changes in version 1.17.7:

Changes in version 1.17.6:

Changes in version 1.17.5:

Changes in version 1.17.4:

Changes in version 1.17.3:

Changes in version 1.17.2:

Changes in version 1.17.1:

Changes in version 1.17.0:

MSnID

Changes in version 1.3.1:

MSstats

Changes in version 3.0.12:

Changes in version 3.0.9:

Changes in version 3.0.8:

Changes in version 3.0.3:

mzID

Changes in version 1.7.1:

mzR

Changes in version 2.3.3:

Changes in version 2.3.2:

Changes in version 2.3.1:

NanoStringDiff

Changes in version 0.99.0:

NEW FEATURES

nethet

1.1.1: package. Added covariance matrix as output of screen_cvglasso.

nondetects

Changes in version 1.99.0:

npGSEA

Changes in version 1.5.1:

omicade4

Changes in version 1.9.1:

NEW FEATURES

OmicsMarkeR

Changes in version 1.1.0:

OncoSimulR

Changes in version 1.99.9 (2015-10-08):

Changes in version 1.99.8 (2015-10-01):

Changes in version 1.99.7 (2015-09-27):

Changes in version 1.99.6 (2015-09-26):

Changes in version 1.99.5 (2015-06-25):

Changes in version 1.99.4 (2015-06-22):

Changes in version 1.99.3 (2015-06-19):

Changes in version 1.99.2 (2015-06-19):

Changes in version 1.99.01 (2015-06-17):

Changes in version 1.99.1 (2015-06-18):

Changes in version 1.99.00 (2015-04-23):

openCyto

Changes in version 1.7.1:

Enhancements

PAA

Changes in version 1.3.3 (2015-07-14):

GENERAL

NEW FEATURES

IMPROVEMENTS

MODIFICATIONS

BUG FIXES

Changes in version 1.3.2 (2015-06-22):

GENERAL

NEW FEATURES

IMPROVEMENTS

MODIFICATIONS

BUG FIXES

Changes in version 1.3.1 (2015-06-17):

GENERAL

NEW FEATURES

IMPROVEMENTS

MODIFICATIONS

BUG FIXES

pandaR

Changes in version 3.2.0:

pathview

Changes in version 1.9.3:

Changes in version 1.9.1:

Pbase

Changes in version 0.9.1:

Changes in version 0.9.0:

PECA

Changes in version 1.5.2 (2015-08-07):

ADDED FUNCTIONS

PGA

Changes in version 0.1.0:

PhenStat

Changes in version 2.3.1:

NEW FUNCTIONALITY

COMPATIBILITY ISSUES

phyloseq

Changes in version 1.13.6:

BUG FIXES

Changes in version 1.13.5:

USER-VISIBLE CHANGES

Changes in version 1.13.4:

BUG FIXES

piano

Changes in version 1.10:

podkat

Changes in version 1.1.3:

Changes in version 1.1.2:

Changes in version 1.1.1:

Changes in version 1.1.0:

polyester

1.99.3: NB function now exported

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

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

pRoloc

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:

Changes in version 1.9.0:

pRolocGUI

Changes in version 1.3.2:

Changes in version 1.3.1:

Changes in version 1.3.0:

Prostar

Changes in version 0.99.0:

ProteomicsAnnotationHubData

Changes in version 0.99.3:

Changes in version 0.99.2:

Changes in version 0.99.1:

Changes in version 0.99.0:

ProtGenerics

Changes in version 1.1.1:

Changes in version 1.1.0:

PWMEnrich

Changes in version 4.5.1:

pwOmics

Changes in version 1.1.10:

Changes in version 1.1.1:

QDNAseq

Changes in version 1.6.0:

RELEASE

IMPROVEMENTS

BUG FIXES

Changes in version 1.4.2 (2015-08-20):

BUG FIXES

Changes in version 1.4.1 (2015-06-30):

IMPROVEMENTS

qpgraph

Changes in version 2.40:

BUG FIXES

QuasR

Changes in version 1.10.0:

NEW FEATURES

qvalue

Changes in version 2.1.1:

R3CPET

1.2.0: Updates: * Removed dependency from DAVIDQuery package as it will deprected. * Fixed some bugs in DAVIDQuery functions and integrated them into R3CPET. * Updated the Readme.Rd file. * Updated the HPRD.RData and Biogrid.RData to the new igraph class. * some small changes.

RCyjs

Changes in version 1.9.8:

BUG FIXES

ReactomePA

Changes in version 1.13.5:

Changes in version 1.13.4:

Changes in version 1.13.3:

Changes in version 1.13.2:

Changes in version 1.13.1:

regioneR

Changes in version 1.1.8:

NEW FEATURES

PERFORMANCE IMPROVEMENTS

BUG FIXES

regionReport

Changes in version 1.3.8:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.3.7:

NEW FEATURES

Changes in version 1.3.6:

NEW FEATURES

Changes in version 1.3.5:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.3.4:

NEW FEATURES

Changes in version 1.3.3:

NEW FEATURES

Changes in version 1.3.2:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.3.1:

BUG FIXES

rGREAT

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:

rhdf5

Changes in version 2.14.0:

NEW FEATURES

BUG FIXES

RiboProfiling

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:

RNAprobR

Changes in version 1.1.2:

BUG FIXES

MISC

RnBeads

Changes in version 1.1.9:

Changes in version 1.1.8:

Changes in version 1.1.7:

Changes in version 1.1.6:

Changes in version 1.1.5:

Changes in version 1.1.4:

Changes in version 1.1.3:

Changes in version 1.1.2:

rols

Changes in version 1.11.6:

Changes in version 1.11.5:

Changes in version 1.11.4:

Changes in version 1.11.3:

Changes in version 1.11.2:

Changes in version 1.11.1:

Changes in version 1.11.0:

ropls

Changes in version 1.1.11:

NEW FEATURES

Changes in version 1.1.10:

NEW FEATURES

Changes in version 1.1.9:

NEW FEATURES

Changes in version 1.1.8:

SIGNIFICANT USER-VISIBLE CHANGES

Changes in version 1.1.7:

NEW FEATURES

Changes in version 1.1.6:

NEW FEATURES

Changes in version 1.1.5:

NEW FEATURES

Changes in version 1.1.4:

NEW FEATURES

Changes in version 1.1.3:

NEW FEATURES

Changes in version 1.1.2:

BUG FIXES

Changes in version 1.1.1:

SIGNIFICANT USER-VISIBLE CHANGES

rpx

Changes in version 1.5.1:

Changes in version 1.5.0:

Rqc

Changes in version 1.4:

NEW FEATURES

USER VISIBLE CHANGES

Rsamtools

Changes in version 1.21:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

Rsubread

Changes in version 1.20.0:

NEW FEATURES

rtracklayer

Changes in version 1.30:

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

RUVSeq

Changes in version 1.3:

sbgr

Changes in version 1.0.0 (2015-05-01):

seq2pathway

Changes in version 1.1.8:

Changes in version 1.1.6:

Changes in version 1.1.4:

Changes in version 1.1.2:

Changes in version 1.0.2:

SeqArray

Changes in version 1.10.0:

SeqVarTools

Changes in version 1.7.9:

Changes in version 1.7.7:

Changes in version 1.7.6:

Changes in version 1.7.5:

Changes in version 1.7.4:

Changes in version 1.7.3:

SGSeq

Changes in version 1.4.0:

ShortRead

Changes in version 1.27:

SIGNIFICANT USER-VISIBLE CHANGES

sincell

Changes in version 1.1.01:

SNPhood

Changes in version 0.99.0 (2015-08-07):

SNPRelate

Changes in version 1.4.0:

specL

Changes in version 1.3.7:

USER UNVISIBLE CHANGES

Changes in version 1.3.5:

USER UNVISIBLE CHANGES

Changes in version 1.3.4:

USER VISIBLE CHANGES

USER UNVISIBLE CHANGES

Changes in version 1.3.3:

USER VISIBLE CHANGES

USER UNVISIBLE CHANGES

Changes in version 1.3.2:

USER VISIBLE CHANGES

Changes in version 1.3.1:

USER VISIBLE CHANGES

USER UNVISIBLE CHANGES

subSeq

Changes in version 1.0.0:

supraHex

Changes in version 1.7.3:

NEW FEATURES

Changes in version 1.7.2:

NEW FEATURES

synapter

Changes in version 1.11.2:

Changes in version 1.11.1:

systemPipeR

Changes in version 1.3:

OVERVIEW

NGS WORKFLOWS

WORFLOW FRAMEWORK

TargetSearch

Changes in version 1.26.0:

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

TarSeqQC

Changes in version 0.99.9:

CODE

Changes in version 0.99.8:

CODE

Changes in version 0.99.7:

CODE

Changes in version 0.99.6:

CODE

Changes in version 0.99.4:

DESCRIPTION file

Changes in version 0.99.3:

CODE

Changes in version 0.99.2:

CODE

Changes in version 0.99.1:

DOCUMENTATION

Changes in version 0.99.0:

DOCUMENTATION

TCC

Changes in version 1.9.3:

TEQC

Changes in version 3.9.1:

TFBSTools

Changes in version 1.7.2:

NEW FEATURES

BUG FIXES

TPP

Changes in version 1.9.9:

Changes in version 1.2.5:

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 1.5.6:

Changes in version 1.5.5:

NEW FEATURES

BUG FIXES

Changes in version 1.5.4:

NEW FEATURES

BUG FIXES

Changes in version 1.5.3:

NEW FEATURES

BUG FIXES

Changes in version 1.5.2:

NEW FEATURES

BUG FIXES

trigger

Changes in version 1.15.1:

TRONCO

Changes in version 2.0.0-16:

variancePartition

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 0.99.0:

VariantAnnotation

Changes in version 1.16.0:

NEW FEATURES

MODIFICATIONS

BUG FIXES

VariantFiltering

Changes in version 1.6:

USER VISIBLE CHANGES

BUG FIXES

xcms

Changes in version 1.45.7:

USER VISIBLE CHANGES

Changes in version 1.45.6:

NEW FEATURE

BUG FIXES

Changes in version 1.45.5:

USER VISIBLE CHANGES

BUG FIXES

Changes in version 1.45.4:

BUG FIXES

Changes in version 1.45.3:

NEW FEATURE

USER VISIBLE CHANGES

BUG FIXES

Changes in version 1.45.2:

BUG FIXES

Changes in version 1.45.1:

NEW FEATURE

xps

Changes in version 3.2:

VERSION xps-1.29.1

yaqcaffy

Changes in version 1.29.1:

Packages removed since the last release

No packages were removed in this release.