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sigaR specifications

Information


Unique identifier OMICS_26995
Name sigaR
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 1.28.0
Stability Stable
Requirements
limma, methods, stats, graphics, Biobase, MASS, snowfall, mvtnorm, quadprog, marray, igraph, CGHbase, penalized, CGHcall, corpcor(>=1.6.2)
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Wessel van Wieringen

sigaR citations

 (3)
library_books

Reduced genomic tumor heterogeneity after neoadjuvant chemotherapy is related to favorable outcome in patients with esophageal adenocarcinoma

2016
Oncotarget
PMCID: 5190081
PMID: 27286451
DOI: 10.18632/oncotarget.9857

[…] 20154) [, ]. All raw datasets were pre-processed and segmented following the same procedures as used in this study. The genomic locations of CGH probes across studies were matched using the R-package sigaR [] and a mean segmented data profile (average across samples) was generated for each data set ().Next, we quantified the degree of genomic tumor heterogeneity for each case by assessing the over […]

library_books

HCsnip: An R Package for Semi supervised Snipping of the Hierarchical Clustering Tree

2015
Cancer Inform
PMCID: 4372030
PMID: 25861213
DOI: 10.4137/CIN.S22080

[…] nt the samples’ features. Missing values are allowed.method: The type of method used to calculate the sample’s molecular entropy. Either “knn” (default) or “normal.” See the hdEntropy function in the sigaR package.parti: A partition for which the violin plot is to be made.horizontal: Should boxes be organized horizontally? Its default value is set to “FALSE.”col: A vector of colors for each cluste […]

library_books

Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses

2012
BMC Bioinformatics
PMCID: 3475006
PMID: 22559006
DOI: 10.1186/1471-2105-13-80

[…] ching as labels of BACs, the DNA copy number probes of the Chin data set, and microRNA probes need not map to a gene label).The results of application of the matching procedures as implemented in the sigaR-package to the five data sets are presented in Table . In all data sets the distance procedure is most successful in terms of the number of gene expression features that have been matched to a D […]

Citations

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sigaR institution(s)
Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands; Department of Mathematics, VU University Amsterdam, Amsterdam, The Netherlands

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