[BioC] Bioconductor 2.9 is released
Dan Tenenbaum
dtenenba at fhcrc.org
Tue Nov 1 22:54:38 CET 2011
Bioconductors:
We are pleased to announce Bioconductor 2.9, consisting of 517
software packages and more than 500 up-to-date annotation packages.
There are 60 new software packages, and many updates and improvements
to existing packages; 10 packages have been removed from this
release. Bioconductor 2.9 is compatible with R 2.14.0, and is
supported on Linux, 32- and 64-bit Windows, and Mac OS. This release
includes an updated Bioconductor Amazon Machine Image. Visit
http://bioconductor.org for details and downloads.
Contents
--------
* Getting Started with Bioconductor 2.9
* New Software Packages
For the full release announcement, including package NEWS and a list
of packages removed from the release, please visit the BioC 2.9 release
page:
http://bioconductor.org/news/bioc_2_9_release/
Getting Started with Bioconductor 2.9
=====================================
To install Bioconductor 2.9:
1. Install R 2.14.0. Bioconductor 2.9 has been designed expressly for
this version of R.
2. Follow the instructions at http://bioconductor.org/install/.
New Software Packages
=====================
There are 60 new packages in this release of Bioconductor.
- AGDEX: Agreement of Differential Expression Analysis
- BiocInstaller: Install/Update Bioconductor and CRAN Packages
- biovizBase: Basic graphic utilities for visualization of genomic
data.
- CellNOptR: R version of CellNOpt, boolean features only
- CNAnorm: A normalization method for Copy Number Aberration in
cancer samples.
- cn.mops: Mixture of Poisson for CNV detection in NGS data
- Cormotif: Correlation Motif Fit
- cqn: Conditional quantile normalization
- cummeRbund: cummeRbund: The finishing touch on your Tuxedo
workflow. Analysis, exploration, manipulation, and visualization of
Cufflinks HTS data.
- DECIPHER: Database Enabled Code for Ideal Probe Hybridization
Employing R
- DEXSeq: Inference of differential exon usage in RNA-Seq
- DiffBind: Differential Binding Analysis of ChIP-Seq peak data
- dks: The double Kolmogorov-Smirnov package for evaluating multiple
testing procedures.
- DOSE: Disease Ontology Semantic and Enrichment analysis
- DTA: Dynamic Transcriptome Analysis
- EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq
- exomeCopy: Detection of CNV in exome/targeted sequencing data
- fastseg: fastseg - a fast segmentation algorithm
- flowType: Phenotyping Flow Cytometry Assays
- flowWorkspace: Import flowJo Workspaces into BioConductor and
replicate flowJo gating with flowCore
- GeneExpressionSignature: Gene Expression Signature based Similarity
Metric
- ggbio: Static visualization for genomic data.
- GOFunction: GO-function: deriving biologcially relevant functions
from statistically significant functions
- graphite: GRAPH Interaction from pathway Topological Environment
- GRENITS: Gene Regulatory Network Inference Using Time Series
- GWASTools: GWASTools: Tools for Genome Wide Association Studies
- htSeqTools: Quality Control, Visualization and Processing for
High-Throughput Sequencing data
- IdMappingRetrieval: ID Mapping Data Retrieval
- inSilicoDb: Access to the InSilico Database
- iontree: Data management and analysis of ion trees from ion-trap
mass spectrometry
- isobar: Analysis and quantitation of isobarically tagged MSMS
proteomics data
- minfi: Analyze Illumina's 450k methylation arrays
- MmPalateMiRNA: Murine Palate miRNA Expression Analysis
- mzR: parser for netCDF, mzXML, mzData and mzML files (mass
spectrometry data)
- ncdfFlow: ncdfFlow: A package that provides ncdf based storage
based flow cytometry data.
- NormqPCR: Functions for normalisation of RT-qPCR data
- nucleR: Nucleosome positioning package for R
- PAN: Posterior association networks and functional modules inferred
from rich phenotypes of gene perturbations
- PREDA: Position RElated Data Anlysis
- predictionet: Inference for predictive networks designed for (but
not limited to) genomic data
- qtbase: Interface between R and Qt
- qtpaint: Qt-based painting infrastructure
- r3Cseq: Analysis of Chromosome Conformation Capture and
Next-generation Sequencing (3C-seq)
- RamiGO: AmiGO visualize R interface
- randPack: Randomization routines for Clinical Trials
- RCASPAR: A package for survival time prediction based on a
piecewise baseline hazard Cox regression model.
- ReadqPCR: Read qPCR data
- RedeR: RedeR: bridging the gap between hierarchical network
representation and functional analysis.
- REDseq: Analysis of high-throughput sequencing data processed by
restriction enzyme digestion
- Repitools: Epigenomic tools
- ReQON: Recalibrating Quality Of Nucleotides
- rqubic: Qualitative biclustering algorithm for expression data
analysis in R
- RTopper: This package is designed to perform Gene Set Analysis
across multiple genomic platforms
- stepwiseCM: Stepwise Classification of Cancer Samples using
Clinical and Molecular Data
- Streamer: Enabling stream processing of large files
- sva: Surrogate Variable Analysis
- TSSi: Transcription Start Site Identification
- tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family
of distributions
- VariantAnnotation: Annotation of Genetic Variants
- zlibbioc: An R packaged zlib-1.2.5
More information about the Bioconductor
mailing list