{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T19:58:01Z","timestamp":1782763081721,"version":"3.54.5"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: \u00a0comb-p is a command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-values) and (5) assigns significance to those regions. In addition, tools are provided for visualization and assessment. We provide validation and example uses on bisulfite-seq with P-values from Fisher\u2019s exact test, tiled methylation probes using a linear model and Dam-ID for chromatin binding using moderated t-statistics. Because the library accepts input in a simple, standardized format and is unaffected by the origin of the P-values, it can be used for a wide variety of applications.<\/jats:p><jats:p>Availability: \u00a0comb-p is maintained under the BSD license. The documentation and implementation are available at https:\/\/github.com\/brentp\/combined-pvalues.<\/jats:p><jats:p>Contact: \u00a0bpederse@gmail.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts545","type":"journal-article","created":{"date-parts":[[2012,9,7]],"date-time":"2012-09-07T01:09:09Z","timestamp":1346980149000},"page":"2986-2988","source":"Crossref","is-referenced-by-count":419,"title":["Comb-p: software for combining, analyzing, grouping and correcting spatially correlated<i>P<\/i>-values"],"prefix":"10.1093","volume":"28","author":[{"given":"Brent S.","family":"Pedersen","sequence":"first","affiliation":[{"name":"1 Department of Medicine and 2Department of Biostatistics and Informatics, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A.","family":"Schwartz","sequence":"additional","affiliation":[{"name":"1 Department of Medicine and 2Department of Biostatistics and Informatics, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivana V.","family":"Yang","sequence":"additional","affiliation":[{"name":"1 Department of Medicine and 2Department of Biostatistics and Informatics, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katerina J.","family":"Kechris","sequence":"additional","affiliation":[{"name":"1 Department of Medicine and 2Department of Biostatistics and Informatics, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,9,5]]},"reference":[{"key":"2023012513223165400_bts545-B1","doi-asserted-by":"crossref","first-page":"3887","DOI":"10.1242\/dev.055871","article-title":"Hedgehog targets in the Drosophila embryo and the mechanisms that generate tissue-specific outputs of Hedgehog signaling","volume":"137","author":"Biehs","year":"2010","journal-title":"Development"},{"key":"2023012513223165400_bts545-B2","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1080\/00031305.1948.10483405","article-title":"Questions and answers #14","volume":"2","author":"Fisher","year":"1948","journal-title":"Am. 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