CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.
Bioinformatics
; 26(21): 2792-3, 2010 Nov 01.
Article
en En
| MEDLINE
| ID: mdl-20810601
ABSTRACT
SUMMARY:
Coordinated Gene Activity in Pattern Sets (CoGAPS) provides an integrated package for isolating gene expression driven by a biological process, enhancing inference of biological processes from transcriptomic data. CoGAPS improves on other enrichment measurement methods by combining a Markov chain Monte Carlo (MCMC) matrix factorization algorithm (GAPS) with a threshold-independent statistic inferring activity on gene sets. The software is provided as open source C++ code built on top of JAGS software with an R interface.AVAILABILITY:
The R package CoGAPS and the C++ package GAPS-JAGS are provided open source under the GNU Lesser Public License (GLPL) with a users manual containing installation and operating instructions. CoGAPS is available through Bioconductor and depends on the rjags package available through CRAN to interface CoGAPS with GAPS-JAGS. URL http//www.cancerbiostats.onc.jhmi.edu/cogaps.cfm .
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Expresión Génica
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Análisis de Secuencia por Matrices de Oligonucleótidos
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Genómica
Tipo de estudio:
Health_economic_evaluation
/
Prognostic_studies
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2010
Tipo del documento:
Article
País de afiliación:
Estados Unidos