EDASeq pipeline

EDASeq specifications

Information


Unique identifier OMICS_01231
Name EDASeq
Alternative name Exploratory Data Analysis and Normalization for RNA-Seq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data RNA-Seq read data
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.8
Stability Stable
Requirements Biobase, ShortRead
Maintained Yes

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Documentation


EDASeq IN pipelines

 (5)
2017
PMCID: 5264326
PMID: 28118819
DOI: 10.1186/s12864-016-3433-4

[…] of 28% and the vast majority of measurements under 40% for all ranges of log2cpm., the quality of the raw data was assessed by principle component analysis using the software r/bioconductor software edaseq [20]. principle component analysis shows that the data is well separated on principle component axis 1 (80%) and fairly well on axis 2., gene set enrichment was performed using […]

2017
PMCID: 5394545
PMID: 28417961
DOI: 10.1038/srep46577

[…] co., ltd. (guangzhou, china). paired-end reads were aligned to the mouse transcriptome with tophat2 as previously described50. rna-seq data were normalized for gc (guanine-cytosine) content with edaseq software. the whole samples expression levels were presented as rpkm (expected number of reads per kilobase of transcript sequence per million base pairs sequenced), which is the recommended […]

2016
PMCID: 4824866
PMID: 26785728
DOI: 10.1074/mcp.M115.054122

[…] (life technologies) and reference genome grch37/hg19. statistical analysis was performed with r (25). normalization and differential expression calculations were carried out using the r packages edaseq (26) and deseq (27), respectively., phosphomannomutase activity was determined as the turnover rate of man-6-p to man-1,6-p in the presence of cofactor glu-1,6-p. twelve micrograms protein […]

2016
PMCID: 5068952
PMID: 27558663
DOI: 10.1534/g3.116.034595

[…] counts for each gene in each sample were computed using htseq (v0.6.1p1) (anders et al. 2015). r software was used for further quality assessment and statistical analysis (r-core-team 2012). the edaseq package was used to plot principal components (risso et al. 2011), and one replicate sample (hrnaif1) was identified as a technical outlier, removed, and the remaining 31 samples were used […]

2015
PMCID: 4549557
PMID: 26379685
DOI: 10.3389/fpls.2015.00657

[…] substantial impact on the read abundances in a rna-seq data set (zheng et al., 2011), counts were full-quantile normalized within sample by the gc content bias correction methods implemented in the edaseq r package (risso et al., 2011). these normalized counts were used to calculate the expression level of each gene (in rpkm units) according to (mortazavi et al., 2008)., conceived and designed […]

EDASeq institution(s)
Department of Statistical Sciences, University of Padua, Italy; Department of Genetics, Stanford University, Standford, CA, USA; Division of Biostatistics and Department of Statistics, University of California, Berkeley, CA, USA
EDASeq funding source(s)
This work was funded by grant R01 HG03468 from the NHGRI at the NIH and grant CPDA094285 from the University of Padua.

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