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This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see easyRNASeq.

Count summarization and normalization for RNA-Seq data

Bioconductor version: 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 <nicolas.delhomme at>

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


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PDF R Script easyRNASeq
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biocViews GeneExpression, Genetics, Preprocessing, RNASeq, Software
Version 2.8.2
In Bioconductor since BioC 2.10 (R-2.15) (4.5 years)
License Artistic-2.0
Imports Biobase(>= 2.31.3), BiocGenerics(>= 0.17.2), BiocParallel(>= 1.5.1), biomaRt(>= 2.27.2), Biostrings(>= 2.39.3), DESeq(>= 1.23.0), edgeR(>= 3.13.4), GenomeInfoDb(>= 1.7.3), genomeIntervals(>= 1.27.0), GenomicAlignments(>= 1.7.3), GenomicRanges(>= 1.23.16), SummarizedExperiment(>= 1.1.11), graphics, IRanges(>= 2.5.27), LSD (>= 3.0), locfit, methods, parallel, Rsamtools(>= 1.23.1), S4Vectors(>= 0.9.38), ShortRead(>= 1.29.1), utils
Suggests BiocStyle(>= 1.9.2), BSgenome(>= 1.39.0), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.4.0), curl, GenomicFeatures(>= 1.23.15), knitr, rmarkdown, RnaSeqTutorial(>= 0.9.0), RUnit (>= 0.4.31)
Depends On Me RnaSeqTutorial
Imports Me
Suggests Me SeqGSEA
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