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comb-p specifications

Information


Unique identifier OMICS_11806
Name comb-p
Alternative name combined-pvalues
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Brent Pedersen <>

Publication for combined-pvalues

comb-p in pipeline

2017
PMCID: 5627482
PMID: 29026448
DOI: 10.1186/s13148-017-0408-5

[…] pathways related to brain development, general cellular functions, and tight junctions., we based the selection of the gabbr1 gene for further validation on the merged analysis from both dmrcate and comb-p, two methods that use different strategies to identify dmrs using hm450 data. although absolute dna methylation differences appeared small, cohen’s d effect sizes in the region were medium […]


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comb-p in publications

 (21)
PMCID: 5896137
PMID: 29682088
DOI: 10.1186/s13148-018-0484-1

[…] spectra were acquired using the massarray® analyzer instrument, and raw data were processed with typeranalyzer software according to the massarray® analyzer user’s guide., dmrs were identified with comb-p analysis [], using the list of uncorrected p values for all cpg sites as calculated from the differential methylation analysis together with their chromosomal location. this statistical […]

PMCID: 5870497
PMID: 29580210
DOI: 10.1186/s12864-018-4594-0

[…] a pipeline for the identification of differentially methylated regions (dmrs). raw p-values for individual cpg sites within each region designated by the bumphunter package were combined using the comb-p software [] and regional p-values were corrected for multiple testing. the comb-p package first calculates the correlation between proximal p-values of varying distances. […]

PMCID: 5802688
PMID: 29249830
DOI: 10.1038/s41398-017-0026-1

[…] we performed the differentially methylated region (dmr) analysis on the combined results from both samples based on the input of individual p-values of at least 5e-05 and within 500 bp using comb-p., a high number of studies showed mostly single snp associations in different genes with pd, however, the replicability of these findings was low. therefore, we used three lines of approaches […]

PMCID: 5627482
PMID: 29026448
DOI: 10.1186/s13148-017-0408-5

[…] (ora) method in erminej with a minimum gene set of 5, and a maximum of 100 []., in order to verify the top dmrs from the dmrcate analysis, we used a second region-specific method: the python module comb-p []. comb-p employs probe locations and p values from the differentially methylated cpg probe (dmp) analysis as input to identify differentially methylated regions. we, therefore, first […]

PMCID: 5604137
PMID: 28923016
DOI: 10.1186/s12864-017-4091-x

[…] ddhps (n = 1278 (58.60%)) compared to hyperhydroxymethylated ddhps (n = 903 (41.40%)) (enrichment hyperhydroxymethylated or = 0.71, p-value = 1.29e-08) (additional file : table s6). we next used comb-p [] to identify spatially correlated regions of developmentally dynamic 5hmc (or developmentally differentially hydroxymethylated regions (ddhrs)). a total of 254 ddhrs (šidák-corrected p-value […]


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comb-p institution(s)
Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO, USA; Department of Biostatistics and Informatics, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO, USA
comb-p funding source(s)
The National Institutes of Health (AA016922, HL101251, AI90052 and HL101715)

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