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Count summarization and normalization for RNA-Seq data.

Bioconductor version: 2.14

Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.

Author: Nicolas Delhomme, Ismael Padioleau, Bastian Schiffthaler

Maintainer: Nicolas Delhomme <delhomme at>

Citation (from within R, enter citation("easyRNASeq")):


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PDF R Script easyRNASeq
PDF   Reference Manual
Text   NEWS


biocViews GeneExpression, Genetics, Preprocessing, RNASeq, Software
Version 2.0.8
In Bioconductor since BioC 2.10 (R-2.15)
License Artistic-2.0
Imports Biobase(>= 2.24.0), BiocGenerics(>= 0.10.0), biomaRt(>= 2.20.0), Biostrings(>= 2.32.1), DESeq(>= 1.16.0), edgeR(>= 3.6.6), genomeIntervals(>= 1.20.1), GenomicAlignments(>= 1.0.2), GenomicRanges(>= 1.16.3), graphics, IRanges(>= 1.22.9), LSD (>= 2.5), methods, parallel, Rsamtools(>= 1.16.1), ShortRead(>= 1.22.0), utils
Suggests BiocStyle(>= 1.2.0), BSgenome(>= 1.32.0), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.1000), GenomicFeatures(>= 1.16.2), RnaSeqTutorial(>= 0.2.0), RUnit (>= 0.4.26)
System Requirements
Depends On Me RnaSeqTutorial
Imports Me
Suggests Me SeqGSEA

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Package Source easyRNASeq_2.0.8.tar.gz
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Mac OS X 10.6 (Snow Leopard) easyRNASeq_2.0.8.tgz
Mac OS X 10.9 (Mavericks) easyRNASeq_2.0.8.tgz
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