R-Gada protocols

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R-Gada specifications

Information


Unique identifier OMICS_07496
Name R-Gada
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for R-Gada

R-Gada in pipeline

2015
PMCID: 4510559
PMID: 26197066
DOI: 10.1371/journal.pone.0133465

[…] to the resulting segments depending upon whether mean lrr is smaller or larger than zero. vega (version 1.7.0) was run using r 2.15 and apt-derived lrr values (see above)., while penncnv, quantisnp, r-gada and vega report a list of segments and their respective cn state, apt and glad output a list of markers and their cn states. to allow comparison between tools, we converted all output to lists […]


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R-Gada in publications

 (8)
PMCID: 5301398
PMID: 28183275
DOI: 10.1186/s12864-017-3531-y

[…] using the nimblegen deva software supplemented with corrections for the gc-content [] of the probes and for wave artifacts along the chromosomes []. we used three different cnv calling methods (r-gada, dnacopy, copymap) to detect high confidence cnvs [–]. the resulting cnv profiles were then merged per individual and only cnvs called by at least two methods were included in our analysis. […]

PMCID: 4707342
PMID: 27057136
DOI: 10.1155/2015/412068

[…] of both a and b alleles, respectively. detection of copy neutral loss of heterozygosity (cnloh) and copy number alterations (gain and loss) was performed using cnvpartition v3.0.7.0 (illumina) and r-gada (r-genome alteration detection analysis) [], respectively, with default parameters., total rna samples were subjected to gene expression microarray analysis using the whole human genome […]

PMCID: 4510559
PMID: 26197066
DOI: 10.1371/journal.pone.0133465

[…] the european and african hapmap trio data, we undertook a comparative evaluation of six commonly used cnv detection software tools, namely affymetrix power tools (apt), quantisnp, penncnv, glad, r-gada and vega, and assessed their level of pair-wise prediction concordance. the tool-specific cnv prediction accuracy was assessed in silico by way of intra-familial validation. software tools […]

PMCID: 5536222
PMID: 24777449
DOI: 10.1038/ng.2966

[…] was used as threshold (mlrr-y of -0.139 in ulsam and -0.154 in pivus)., the percentage of cells containing a structural variant was calculated using mad-software. mad is included in the r-package r-gada and is used in snp data analysis to identify regions containing deletions, gains and cnnloh. r-gada is detecting allelic imbalances caused by genetic abnormalities using a cbs-based […]

PMCID: 3849454
PMID: 24053169
DOI: 10.1186/1755-8794-6-33

[…] intensities, log r ratio (lrr) and b allele frequency (baf)), quality scores and to call genotypes. renormalized (quantile) lrr and baf values were then analyzed using a custom software pipeline, r-gada [], to detect whole-chromosome and segmental events as previously described []., we only observed chromosomal copy number alterations in the panc-1 cell line but not in the htert-hpne cells. […]


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R-Gada institution(s)
Signal and Image Processing Institute, Viterbi School of Engineering, University of Southern California, McClintock Ave, Los Angeles, CA, USA

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