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This is the development version of easyRNASeq; for the stable release version, see easyRNASeq.

Count summarization and normalization for RNA-Seq data

Bioconductor version: Development (3.3)

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, Niklas Maehler

Maintainer: Nicolas Delhomme <delhomme at>

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


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PDF easyRNASeq
PDF   Reference Manual
Text   NEWS


biocViews GeneExpression, Genetics, Preprocessing, RNASeq, Software
Version 2.7.0
In Bioconductor since BioC 2.10 (R-2.15) (3.5 years)
License Artistic-2.0
Imports Biobase(>= 2.29.1), BiocGenerics(>= 0.15.3), BiocParallel(>= 1.3.29), biomaRt(>= 2.25.1), Biostrings(>= 2.37.2), DESeq(>= 1.21.0), edgeR(>= 3.11.2), GenomeInfoDb(>= 1.5.8), genomeIntervals(>= 1.25.3), GenomicAlignments(>= 1.5.11), GenomicRanges(>= 1.21.16), SummarizedExperiment(>= 0.3.1), graphics, IRanges(>= 2.3.23), LSD (>= 3.0), locfit, methods, parallel, Rsamtools(>= 1.21.11), S4Vectors(>= 0.7.21), ShortRead(>= 1.27.4), utils
Suggests BiocStyle(>= 1.7.4), BSgenome(>= 1.37.2), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.4.0), GenomicFeatures(>= 1.21.13), RnaSeqTutorial(>= 0.7.0), RUnit (>= 0.4.28)
Depends On Me RnaSeqTutorial
Imports Me
Suggests Me SeqGSEA
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