RUVSeq protocols

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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 1.15.1
Stability Stable
Requirements
methods, RColorBrewer, Biobase, BiocStyle, edgeR, DESeq2, knitr, MASS, zebrafishRNASeq, EDASeq(>=1.99.1)
Maintained Yes

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Maintainer


  • person_outline Sandrine Dudoit <>

Publication for RUVSeq

RUVSeq in pipelines

 (9)
2017
PMCID: 5578099
PMID: 28777335
DOI: 10.3390/ijms18081709

[…] of the aligned reads were summarized by htseq (v0.6.1, california institute of technology, pasadena, ca, usa) []. 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 []. 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: 5685552
PMID: 29147574
DOI: 10.1093/eep/dvx016

[…] bowtie2 [] with default parameter options. the mapped read files were then converted to sorted bam files using samtools []. to identify dmrs, the reference genome was broken into 100 bp windows. the ruvseq r package was used for ruv normalization []. the medips r package [] was used to calculate differential coverage between control and exposure sample groups. the edger p-value [] was used […]

2017
PMCID: 5719936
PMID: 29212455
DOI: 10.1186/s12885-017-3832-1

[…] for 522 lung adenocarcinoma patient tissues in the cancer genome atlas project (tcga-luad) and 320 healthy lung tissues in genotype-tissue expression (gtex) project were normalized using r package, ruvseq []. the differential expression analysis that calculated the logfc values for all genes was completed using r package, edger []., given a tcga patient and an emt time-series gene expression […]

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 […]


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RUVSeq in publications

 (36)
PMCID: 5943448
PMID: 29743490
DOI: 10.1038/s41598-018-25368-x

[…] as mentioned above). express software was again used to generate total counts for individual libraries for further analysis. we followed a normalization strategy, called remove unwanted variation (ruv), that adjusts for nuisance technical effects by performing factor analysis on suitable sets of control genes (e.g., external rna control consortium (ercc) manual modified on october 17, 2016). […]

PMCID: 5940186
PMID: 29738525
DOI: 10.1371/journal.pone.0196913

[…] annotations using rsubread package, version 1.24.0 [], to generate raw counts for each gene. raw read count data were normalized to ercc spike-in values across samples using bioconductor package ruvseq_1.8.0 []. we removed non-expressed genes by requiring more than 5 reads for each gene. r bioconductor package noiseq was used evaluate and access the quality control of the count data []., […]

PMCID: 5896901
PMID: 29649237
DOI: 10.1371/journal.pone.0194803

[…] normalization of rna-sequences was obtained using the upper-quartile method provided by edaseq package in r bioconductor, followed by removing unwanted variation (ruv) technique using ruvg function provided by r bioconductor package ruvseq, where a set of 20 house keeping genes were used as negative controls []. ruvg has the potential to normalize […]

PMCID: 5880879
PMID: 29611322
DOI: 10.14814/phy2.13653

[…] calculated to scale the raw library sizes and a common negative binomial dispersion parameter estimated using the bioconductor package edger (robinson et al. ; mccarthy et al. ) and normalized using ruvseq (risso et al. ), which reduces the variability in an unbiased manner by estimating variation by residuals. mirna target pathways were identified using the mirpathdb (backes et al. ). the mirna […]

PMCID: 5849806
DOI: 10.1016/j.omtn.2018.01.005

[…] 59b, and so on. we mapped all reads in the non-splice-junction-aware mode. for comparison of mirna expression between samples, a differential expression analysis was performed using r deseq2 and the ruvseq package. small rna sequencing data are accessible at geo: gse109066. heatmaps were created using custom python script for python v.2.7.1 and matplotlib 1.5.1. computational mirna target […]


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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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