- Unique identifier:
- Software type:
- Restrictions to use:
- 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
- Programming languages:
- C++, R
- Computer skills:
- Coordinated Gene Activity in Pattern Sets
- Command line interface
- 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
- Operating system:
- Unix/Linux, Mac OS, Windows
- GNU General Public License version 2.0
No open topic.
(Fertig et al., 2010)
CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.
PMID: 20810601 DOI: 10.1093/bioinformatics/btq503
(Stein-O Brien, 2016)
PatternMarkers and Genome-Wide CoGAPS in Analysis in Parallel Sets (GWCoGAPS) for data-driven detection of novel biomarkers via whole transcriptome Non-negative matrix factorization (NMF).
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
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.
0 user reviews
0 user reviews
No review has been posted.