Bioconductor Task View: HighThroughputSequencing

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Package Maintainer Title
BayesPeak Jonathan Cairns Bayesian Analysis of ChIP-seq Data
baySeq Thomas J. Hardcastle Empirical Bayesian analysis of patterns of differential expression in count data
ChIPpeakAnno Lihua Julie Zhu Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.
chipseq Biocore Team c/o BioC user list chipseq: A package for analyzing chipseq data
ChIPseqR Peter Humburg Identifying Protein Binding Sites in High-Throughput Sequencing Data
ChIPsim Peter Humburg Simulation of ChIP-seq experiments
CSAR Jose M Muino Statistical tools for the analysis of ChIP-seq data
DEGseq Likun Wang Identify Differentially Expressed Genes from RNA-seq data
DESeq Simon Anders Digital gene expresion analysis based on the negative binomial distribution
edgeR Mark Robinson , Davis McCarthy , Gordon Smyth Empirical analysis of digital gene expression data in R
gage Weijun Luo Generally Applicable Gene-set Enrichment for Pathway Analysis
GenomicFeatures Biocore Team c/o BioC user list Tools for making and manipulating transcript centric annotations
GenomicRanges Biocore Team c/o BioC user list Representation and manipulation of genomic intervals
girafe J. Toedling Genome Intervals and Read Alignments for Functional Exploration
goseq Matthew Young Gene Ontology analyser for RNA-seq and other length biased data
MotIV Eloi Mercier , Raphael Gottardo Motif Identification and Validation
oneChannelGUI Raffaele A Calogero This package extends the capabilities of affylmGUI graphical interface. Affymetrix 3' IVT, gene an exon arrays are actually implemented togheter with Illumina, GEO matrix series files and tab delimited files. Next Generation Sequencing secondary analysis for ncRNA quantification is also available.
PICS Arnaud Droit , Xuekui Zhang , Raphael Gottardo Probabilistic inference of ChIP-seq
R453Plus1Toolbox H-U Klein A package for importing and analyzing data from Roche's Genome Sequencer System.
rGADEM Arnaud Droit de novo motif discovery
rnaSeqMap Michal Okoniewski rnaSeq analyses using xmapcore database
Rsamtools Biocore Team c/o BioC user list Import aligned BAM file format sequences into R / Bioconductor
segmentSeq Thomas J. Hardcastle Methods for identifying small RNA loci from high-throughput sequencing data
ShortRead Biocore Team c/o BioC user list Classes and methods for high-throughput short-read sequencing data.
splots Wolfgang Huber Visualization of high-throughput assays in microtitre plate or slide format
SRAdb Jack Zhu A compilation of metadata from NCBI SRA and tools