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Count summarization and normalization for RNA-Seq data.

Bioconductor version: 2.13

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>

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PDF R Script easyRNASeq
PDF   Reference Manual
Text   NEWS


biocViews GeneExpression, Genetics, Preprocessing, RNAseq, Software
Version 1.8.8
In Bioconductor since BioC 2.10 (R-2.15)
License Artistic-2.0
Depends genomeIntervals(>= 1.18.0), Biobase(>= 2.22.0), biomaRt(>= 2.18.0), edgeR(>= 3.4.0), Biostrings(>= 2.30.0), DESeq(>= 1.14.0), GenomicRanges(>= 1.14.3), IRanges(>= 1.20.5), Rsamtools(>= 1.14.1), ShortRead(>= 1.20.0)
Imports graphics, methods, parallel, utils, BiocGenerics(>= 0.8.0), LSD (>= 2.5)
Suggests BSgenome(>= 1.30.0), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.19), GenomicFeatures(>= 1.14.0), RnaSeqTutorial(>= 0.0.13), BiocStyle(>= 1.0.0)
System Requirements
Depends On Me RnaSeqTutorial
Imports Me
Suggests Me

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Package Source easyRNASeq_1.8.8.tar.gz
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Mac OS X 10.6 (Snow Leopard) easyRNASeq_1.8.8.tgz
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