easyRNASeq pipeline

easyRNASeq specifications

Information


Unique identifier OMICS_01938
Name easyRNASeq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.4.2
Stability Stable
Requirements graphics, methods, parallel, utils, genomeIntervals, Biobase, BiocGenerics, biomaRt, edgeR, Biostrings, BSgenome, DESeq, GenomicRanges, IRanges, Rsamtools, ShortRead
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Nicolas Delhomme <>

Publication for easyRNASeq

easyRNASeq IN pipelines

 (2)
2018
PMCID: 5928323
PMID: 29740591
DOI: 10.3389/fcvm.2018.00030

[…] the left end of the r2 reads). sequence alignment was performed using tophat v2.1.0 to the mm10 genome. bam files were merged on a per sample. exon and gene level counting were performed using the easyrnaseq version 2.4.7 package. a binary annotation file, built using the annotation file generation function of easyrnaseq, was used for this analysis; the ensembl release 83 gtf file was used […]

2018
PMCID: 5928323
PMID: 29740591
DOI: 10.3389/fcvm.2018.00030

[…] were merged on a per sample. exon and gene level counting were performed using the easyrnaseq version 2.4.7 package. a binary annotation file, built using the annotation file generation function of easyrnaseq, was used for this analysis; the ensembl release 83 gtf file was used as input. annotation was performed using a gene transfer format (gtf) annotation file for mus musculus, […]

easyRNASeq institution(s)
Genome Biology Computational Support; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
easyRNASeq funding source(s)
Supported by the European Molecular Biology Laboratory, an ERASysBio grant ModHeart and a NIH grant (NIH: R01 GM068717).

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