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RankAggreg specifications

Information


Unique identifier OMICS_03526
Name RankAggreg
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 0.6.5
Stability Stable
Requirements
gtools, xtable, clValid, mclust, R(≥2.12.0), kohonen
Maintained Yes

Versioning


No version available

Documentation


Publication for RankAggreg

RankAggreg citations

 (33)
call_split

Expressed repetitive elements are broadly applicable reference targets for normalization of reverse transcription qPCR data in mice

2018
Sci Rep
PMCID: 5955877
PMID: 29769563
DOI: 10.1038/s41598-018-25389-6
call_split See protocol

[…] stability values for all reference targets (M-value) and to determine the optimal number of reference targets for every experiment (V-value). Graphs were created using GraphPad Prism version 5.04.The Rankaggreg package in R (version 3.2.3) was used to perform rank aggregation analysis. […]

call_split

Selection of reference genes for miRNA qRT PCR under abiotic stress in grapevine

2018
Sci Rep
PMCID: 5849727
PMID: 29535408
DOI: 10.1038/s41598-018-22743-6
call_split See protocol

[…] ng the samples of six time points. Bestkeeper and deltaCt were performed by the online analysis tool RefFinder (http://fulxie.0fees.us/?type=reference). To integrate the ranks of the four algorithms, RankAggreg Rpackage (Version 0.5) was used to generate a consensus ranking of candidate reference genes. […]

call_split

Oncologic emergencies in a cancer center emergency department and in general emergency departments countywide and nationwide

2018
PLoS One
PMCID: 5819770
PMID: 29462166
DOI: 10.1371/journal.pone.0191658
call_split See protocol

[…] OC) curve and its area under the curve (AUC). Ranked lists of relative importance of top contributing factors from randomForest and h2o.randomForest were then combined by rank aggregation (R package “RankAggreg”, version 0.5) to assess the association of those factors with hospitalization through the ED. […]

library_books

Reference gene selection for molecular studies of dormancy in wild oat (Avena fatua L.) caryopses by RT qPCR method

2018
PLoS One
PMCID: 5794185
PMID: 29390041
DOI: 10.1371/journal.pone.0192343

[…] genes either according to the geometric mean of the ranking numbers calculated e.g. by a web-based tool RefFinder [, , ] or the consensus reached with a cross-entropy Monte Carlo algorithm offered by RankAggreg, an R package for weighted rank aggregation [, ]. Robledo et al. [] criticized the motion of selecting the best reference gene(s) due to such consensus rankings as having no biological mean […]

library_books

Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation Induced Bystander Effects (RIBE)

2017
PMCID: 5742808
PMID: 29186820
DOI: 10.3390/cancers9120160

[…] he aim to identify linker genes for diverse scopes in cellular physiology. Starting from the results of BIM gene prioritization for different vocabularies and using them as an input for the R package RankAggreg, a final subset of 28 pivotal genes was derived, representing candidate key-players for RIBE. The robustness of our methodology in this step is not solely limited to the gene expression, bu […]

call_split

Transcription of putative tonoplast transporters in response to glyphosate and paraquat stress in Conyza bonariensis and Conyza canadensis and selection of reference genes for qRT PCR

2017
PLoS One
PMCID: 5507266
PMID: 28700644
DOI: 10.1371/journal.pone.0180794
call_split See protocol

[…] each treatment and species and genes were ranked based on stability. A consensus ranking was calculated using the Monte Carlo algorithm based on the Spearman’s distances across rankings performed by RankAggreg package in R []. The three most stable genes were selected as reference genes to assay the transcript levels of target genes. […]

Citations

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RankAggreg institution(s)
Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY, USA

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