easyRNASeq statistics

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Citations per year

Number of citations per year for the bioinformatics software tool easyRNASeq
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Tool usage distribution map

This map represents all the scientific publications referring to easyRNASeq per scientific context
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Associated diseases

This word cloud represents easyRNASeq usage per disease context
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Popular tool citations

chevron_left Normalization Demultiplexing Known transcript quantification Differential expression Bioinformatics workflows Transcriptome annotation chevron_right
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Protocols

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
methods, parallel, graphics, utils, genomeIntervals(>=1.14.0), Biobase(>=2.18.0), BiocGenerics(>=0.4.0), biomaRt(>=2.14.0), edgeR(>=3.0.0), Biostrings(>=2.26.0), BSgenome(>=1.26.0), DESeq(>=1.10.0), GenomicRanges(>=1.10.0), IRanges(>=1.16.0), Rsamtools(>=1.10.0), ShortRead(>=1.16.0), BSgenome.Dmelanogaster.UCSC.dm3(>=1.3.17), GenomicFeatures(>=1.10.0), RnaSeqTutorial(>=0.0.10)
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Nicolas Delhomme

Publication for easyRNASeq

easyRNASeq citations

 (17)
library_books

Postnatal and Adult Aortic Heart Valves Have Distinctive Transcriptional Profiles Associated With Valve Tissue Growth and Maintenance Respectively

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

[…] at 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 as i […]

library_books

A systems level approach reveals new gene regulatory modules in the developing ear

2017
PMCID: 5399671
PMID: 28264836
DOI: 10.1242/dev.148494

[…] acquired from UCSC table browser as a guide. All assemblies were merged to obtain a merged annotation file, which was passed to Cuffdiff (v2.1.1) to obtain normalized RPKM value for each gene, and to easyRNAseq (v2.1.0) to retrieve the count table for all genes (). All sequencing data were deposited in Gene Expression Omnibus (GEO) under accession number GSE69185. […]

library_books

Sex differences in the molecular signature of the developing mouse hippocampus

2017
BMC Genomics
PMCID: 5356301
PMID: 28302071
DOI: 10.1186/s12864-017-3608-7

[…] ered, sorted and indexed) with Samtools [] and only reads that mapped to a single gene were used for further analysis. Uniquely mapped reads were used to generate counts for each annotated gene using easyRNASeq []. A count table was generated for all samples containing the number of reads for each of the 37,315 annotated genes from the mouse genome. For differential expression analyses, RNA-seq da […]

library_books

A somatic piRNA pathway in the Drosophila fat body ensures metabolic homeostasis and normal lifespan

2016
Nat Commun
PMCID: 5187580
PMID: 28000665
DOI: 10.1038/ncomms13856

[…] Reads were mapped to the dm3 genome using Tophat. The Bioconductor R package easyRNASeq was used to count reads (using ‘geneModels' summarization parameter) and calculate normalized reads per kilobase per million (RPKM) values. Error bars presented represent s.e.m. with three […]

library_books

Global repositioning of transcription start sites in a plant fermenting bacterium

2016
Nat Commun
PMCID: 5171806
PMID: 27982035
DOI: 10.1038/ncomms13783

[…] ch results were compared with strand-specific (dUTP) RNA-seq of C. phytofermentans grown in the same culture conditions. RNA-seq gene expression was calculated as RPKM using the Bioconductor package ‘easyRNASeq' and differential expression was defined as a DESeq (version 1.22.1) P-value <0.05 adjusted for multiple testing of the 3,902 genes in C. phytofermentans genome by Bonferroni correction. Pe […]

call_split

Upregulation of Haploinsufficient Gene Expression in the Brain by Targeting a Long Non coding RNA Improves Seizure Phenotype in a Model of Dravet Syndrome

2016
PMCID: 4972487
PMID: 27333023
DOI: 10.1016/j.ebiom.2016.05.011
call_split See protocol

[…] CASAVA software version 1.83 was used to produce de-multiplexed FASTQ sequence files from raw .bcl files. Sequences were aligned to the human genome version hg19 (UC Santa Cruz) using TopHat v1.4.1. EasyRNASeq v1.6.0 running on the R version 3.0 platform was used for determination of raw reads and reads per kilobase per million reads (RPKM) for each gene and exon. Using a custom R script, further […]


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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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