CoGAPS specifications

Information


Unique identifier OMICS_01973
Name CoGAPS
Alternative name Coordinated Gene Activity in Pattern Sets
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data List or data frame containing the genes in each gene set, number of permutations used for the N/A distribution in the gene set statistic
Output data p-values for upregulation and for downregulation of each gene set in each pattern, conversion of p-values to activity estimates of each gene set in each pattern
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.8.0
Stability Stable
Requirements Rcpp
Maintained Yes

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Documentation


CoGAPS articles

CoGAPS institution(s)
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD; Lieber Institute for Brain Development, Baltimore, MD, USA; Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA; Vavilov Institute of General Genetics, Moscow, Russia; Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia; Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, USA; Department of Neurology and Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
CoGAPS funding source(s)
This work was supported by the National Institutes of Health [NCI R01CA177669 and K25CA141053, NLM R01LM001100 and NCI P30 CA006973] and the Cleveland Foundation and Johns Hopkins University Discovery Awards.

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