RUVSeq protocols

RUVSeq specifications

Information


Unique identifier OMICS_05652
Name RUVSeq
Alternative name RUV
Software type Package/Module
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 1.13
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Sandrine Dudoit <>

Publication for RUVSeq

RUVSeq IN pipelines

 (4)
2017
PMCID: 5457141
PMID: 28489004
DOI: 10.7554/eLife.23253.044

[…] al., 2014) using the uniq-counting mode., differential expression analysis was performed by deseq2 (love et al., 2014). batch effects from library preparation and sequencing were removed using the ruv r package (risso et al., 2014). pathway and functional analysis of gene lists were performed using the go-elite (zambon et al., 2012)., to examine gene expression in arg in human and mouse […]

2017
PMCID: 5578099
PMID: 28777335
DOI: 10.3390/ijms18081709

[…] the aligned reads were summarized by htseq (v0.6.1, california institute of technology, pasadena, ca, usa) [34]. to remove technical variations, the read counts were normalized using the r-package ruvseq (ver. 1.6.0, university of california, berkeley, ca, usa) according to instructions in the manual compiled on 3 may 2016 [14]. the ruvs method was used to estimate the unwanted variation using […]

2017
PMCID: 5684402
PMID: 29133896
DOI: 10.1038/s41598-017-15379-5

[…] cutoff. two biological replicates were sequenced and analyzed for each experimental condition. batch effects, as a result of different sequencing runs, were identified and corrected using ruvseq. genes were categorized using cluster of orthologous groups (cog) categories automated by a custom r script, and enrichment was analyzed using fisher’s exact test. data analysis revealed […]

2017
PMCID: 5910063
PMID: 28825709
DOI: 10.1038/nature23876

[…] using tophat 2.0.12 with bowtie2 2.2.3. mapped reads were quality-filtered using samtools 0.1.19, and quantified using htseq 0.6.1. differential expression was assessed using deseq2 1.8.2 and ruvseq 1.2.0 with r 3.2.1. a fold change heatmap was generated using cluster 3.0. computational analysis was performed using the biohpc high-performance computing cluster at utsw., 10 hscs per well […]

RUVSeq institution(s)
Department of Statistics, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA; Functional Genomics Laboratory, University of California, Berkeley, Berkeley, CA, USA; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Mathematics and Statistics, The University of Melbourne, Victoria, Australia; Department of Statistics, University of California, Berkeley, Berkeley, CA, USA; Division of Biostatistics, University of California, Berkeley, Berkeley, CA, USA
RUVSeq funding source(s)
Supported by a grant from the National Institute on Deafness and Other Communication Disorders. T.P.S. was supported by an NHMRC Australia Fellowship.

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