ArticleBioinformatics (Oxford, England)2010
CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
- Cytometric Atlas of Combination Immunotherapy in Pancreatic Cancer: Blood-Based Signatures Reveal Vaccine and Checkpoint Inhibitor Responses.Cancer immunology research · 2026Article
- Fibroblast STAT3 Activation Drives Organ-Specific Premetastatic Niche Formation.Cancer research · 2026Article
- Comparative assessment of physiochemical metrics for the clustering of adaptive immune receptor repertoires.Nucleic acids research · 2025Article
- Neoadjuvant Immunotherapy Promotes the Formation of Mature Tertiary Lymphoid Structures in a Remodeled Pancreatic Tumor Microenvironment.Cancer immunology research · 2025Article
- Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP.Genome research · 2025Article
- Allelic bias contributes to heterogeneous phenotypes of NK cell deficiency.Cell reports · 2025Article
- Spatial proteomics and transcriptomics reveal early immune cell organization in pancreatic intraepithelial neoplasia.JCI insight · 2025Article
- Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine.Genome medicine · 2025Article
- MOTL: enhancing multi-omics matrix factorization with transfer learning.Genome biology · 2025Article
- mNSF: multi-sample non-negative spatial factorization.Genome biology · 2025Article
- Identification of shared gene expression programs activated in multiple modes of torpor across vertebrate clades.Scientific reports · 2024Article
- PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration.Cell systems · 2024Article
- Interface-guided phenotyping of coding variants in the transcription factor RUNX1.Cell reports · 2024Article
- Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional regulation.Science immunology · 2024Article
- Gene expression signatures in blood from a West African sepsis cohort define host response phenotypes.Nature communications · 2024Article
- Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial-Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma.Cancer research · 2024Article
- Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS.Nature protocols · 2023Review
- Digitize your Biology! Modeling multicellular systems through interpretable cell behavior.bioRxiv : the preprint server for biology · 2023Article
- A primer on correlation-based dimension reduction methods for multi-omics analysis.Journal of the Royal Society, Interface · 2023Review
- Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
summaryCoordinated 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 .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.