RUV protocols

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RUV specifications

Information


Unique identifier OMICS_08543
Name RUV
Alternative name RUVm
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.9.7
Stability Stable
Requirements
stats, ggplot2, scales, shiny, gridExtra, colourpicker
Source code URL https://cran.r-project.org/src/contrib/ruv_0.9.7.tar.gz
Maintained Yes

Versioning


Add your version

Documentation


Maintainers


  • person_outline Johann A. Gagnon-Bartsch <>
  • person_outline Alicia Oshlack <>
  • person_outline Terence Speed <>

Additional information


http://statistics.berkeley.edu/tech-reports/820 http://www-personal.umich.edu/~johanngb/ruv/

Publications for RUV

RUV in pipelines

 (5)
2018
PMCID: 5824607
PMID: 29484035
DOI: 10.1186/s13148-018-0457-4

[…] later became discordant for cp. quality control and data preprocessing were undertaken using the minfi r package. differential methylation analysis was performed using the remove unwanted variation (ruvm) method, taking twin pairing into account in order to identify cp-specific differentially methylated probes (dmps), and bumphunter was performed to identify differentially methylated regions […]

2018
PMCID: 5864071
PMID: 29529020
DOI: 10.1371/journal.pbio.2004328

[…] sfc025, sfd001, and sfm009 excluded due to insufficient coverage., the proportion of parasites present at the ring stage—as well as 3 factors of unwanted variation estimated using the r package ruv []—were used to account for life cycle and other unwanted batch effects. differential expression testing was conducted using the limma/voom pipeline [,]. the impact of including these covariates […]

2017
PMCID: 4916993
PMID: 27347385
DOI: 10.5256/f1000research.9514.r14245

[…] ## [69] checkmate_1.8.2 ## [70] genomicfeatures_1.26.3 ## [71] biocparallel_1.8.1 ## [72] bitops_1.0-6 ## [73] nor1mix_1.2-2 ## [74] evaluate_0.10 ## [75] lattice_0.20-34 ## [76] ruv_0.9.6 ## [77] genomicalignments_1.10.1 ## [78] htmlwidgets_0.8 ## [79] plyr_1.8.4 ## [80] magrittr_1.5 ## [81] r6_2.2.0 ## [82] hmisc_4.0-2 ## [83] dbi_0.6 ## [84] foreign_0.8-67 ## [85] […]

2014
PMCID: 4283580
PMID: 25599564
DOI: 10.1186/s13059-014-0503-2

[…] analysis of data sets with global methylation differences, including studies of human cancer. we also show that functional normalization outperforms the batch removal tools sva [,], combat [] and ruv [] in this setting. our evaluation metrics focus on assessing the degree of replication between large-scale studies, arguably the most important biologically relevant end point for such studies. […]

2014
PMCID: 4283580
PMID: 25599564
DOI: 10.1186/s13059-014-0503-2

[…] most normalization methods, does not require the analyst to provide information about the experimental design. in contrast, supervised normalization methods, such as sva [,], combat [], snm [] and ruv [], require the user to provide either batch parameters or an outcome of interest. like functional normalization, ruv also utilizes control probes as surrogates for batch effects, but builds […]


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RUV in publications

 (18)
PMCID: 5864071
PMID: 29529020
DOI: 10.1371/journal.pbio.2004328

[…] subject to the constraints ∑s∈sπs=1 and πs≥0 such that gi,s represents the expression of the ith gene in stage s of the [] data., three factors of unwanted variation were estimated using the ruv4 function from the r package ruv v0.9.6 [] using the 1,009 genes with the lowest p-values from [] as controls. the choice of control genes was compared to using the least differentially expressed […]

PMCID: 5824607
PMID: 29484035
DOI: 10.1186/s13148-018-0457-4

[…] later became discordant for cp. quality control and data preprocessing were undertaken using the minfi r package. differential methylation analysis was performed using the remove unwanted variation (ruvm) method, taking twin pairing into account in order to identify cp-specific differentially methylated probes (dmps), and bumphunter was performed to identify differentially methylated regions […]

PMCID: 5833693
PMID: 29449600
DOI: 10.1038/s41419-018-0332-4

[…] with background correction using the normexp method (https://www.bioconductor.org/packages/release/bioc/html/limma.html). fold changes and p values were obtained using the ruvinv function from ruv r package, (http://www-personal.umich.edu/~johanngb/ruv/index.html). the list of control genes was from eisenberg et al. the data set and technical information compliant with minimum information […]

PMCID: 5746284
PMID: 29240831
DOI: 10.1371/journal.ppat.1006767

[…] were tested, including a mix of: trimmed median of m-values, quantile, log transformation, and counts per million. surrogate variables / batches were queried with a mix of methods from sva [] and ruv []. differential expression analyses were performed and compared using surrogate estimates from svaseq with limma [], deseq2 [], edger [], and a statistically uninformed basic method […]

PMCID: 5593822
PMID: 28894120
DOI: 10.1038/s41598-017-09552-z

[…] levels strata (triglyceride levels ≥1.12 mmol/l and triglyceride levels <1.12 mmol/l) using a piecewise linear regression model. models were adjusted for age, sex and cell type proportion (ruv component in the f5l family study). ci, confidence interval; n, number of individuals in the stratum. , associations were tested using a linear regression model (a variance components model […]


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RUV institution(s)
Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia; Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia; Department of Statistics, University of Michigan, Ann Arbor, MI, USA; School of Cancer Medicine, La Trobe University, Bundoora, VIC, Australia; Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia; Department of Mathematics and Statistics, University of Melbourne, VIC, Australia
RUV funding source(s)
Supported by Program Grant 1054618 from the National Health and Medical Research Council of Australia; Cancer Australia for the lung cancer DNA repair study, two international Australian postgraduate scholarships (MIRS and MIFRS) from The University of Melbourne and a CTx PhD top up scholarship from the Cancer Therapeutics CRC and by the Victorian Government’s Operational Infrastructure Support Program to the Olivia Newton-John Cancer Research Institute.

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