COHCAP statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Differentially methylated region detection Quality control Methylation scoring Differentially methylated region detection Data integration chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

COHCAP specifications

Information


Unique identifier OMICS_00595
Name COHCAP
Alternative name City of Hope CpG Island Analysis Pipeline
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Perl, R
Computer skills Advanced
Version 1.26.0
Stability Stable
Requirements
RColorBrewer, gplots, Rcpp, WriteXLS, COHCAPanno, RcppArmadillo, BH
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainers


Publication for City of Hope CpG Island Analysis Pipeline

COHCAP in pipeline

2014
PMCID: 4165320
PMID: 25278959
DOI: 10.3389/fgene.2014.00324

[…] et al., ; aryee et al., ) and various options for inferring dm sites from 27k/450k array data have been proposed. to test for dm, ima proposes wilcoxon rank-sum tests on beta-values (wang et al., ). cohcap operates either on methylation array data or bs-seq data, using beta-values or methylation proportions as input; they offer fet (see comment above), t-tests and anova analyses (without […]


To access a full list of citations, you will need to upgrade to our premium service.

COHCAP in publications

 (11)
PMCID: 5943364
PMID: 29743579
DOI: 10.1038/s41598-018-24240-2

[…] for further statistical analysis. beta values are defined as the ratio of methylated probe intensity and overall probe intensity (sum of both unmethylated and methylated probe intensity)., the cohcap algorithm was applied for the statistical analysis of differentially methylated cpg sites and islands. a cpg site was counted as methylated if the beta value was greater than 0.4 […]

PMCID: 5865950
PMID: 29393436
DOI: 10.3892/mmr.2018.8487

[…] pretreatment of the raw data, differentially methylated regions (dmrs) and differentially methylated cpg islands (dmcs) were identified between the npc samples and normal tissue controls using cohcap software. the overlapped dmrs and dmcs in the two data sets were extracted and associated to relevant genes. enrichment analysis and protein-protein interaction (ppi) network analyses […]

PMCID: 5708922
PMID: 29381923
DOI: 10.1097/MD.0000000000008487

[…] methylation for this disease., data were downloaded from the cancer genome atlas database. differentially methylated cpg sites (dmcs) and differentially methylated regions (dmrs) were calculated via cohcap. differentially expressed genes (degs) were identified by deseq2. weighted gene co-expression network analysis (wgcna) package in r was applied for wgcna., data of 275 solid tumor tissues […]

PMCID: 5752236
PMID: 29207054
DOI: 10.3892/ijmm.2017.3271

[…] / (methylated signal + unmethylated signal + 100); a constant bias of 100 was added to regularize the β-value when the methylated signal value and the unmethylated signal values were small ()., the city of hope cpg island analysis pipeline (cohcap) package in bioconductor (https://sourceforge.net/projects/cohcap/) is an algorithm to analyze either illumina methylation array or bisulfite […]

PMCID: 5706906
PMID: 29212260
DOI: 10.18632/oncotarget.21885

[…] according to the from nordlund et al. [], where probes in proximity to snps or at snp-sites were removed. probes on x and y chromosomes were retained. annotation was performed with the r-package cohcap. finally, the beta-values for the remaining 446 412 probes were presented and an average beta-value for each gene was calculated., the statistical analysis of experimental data was performed […]


To access a full list of publications, you will need to upgrade to our premium service.

COHCAP institution(s)
Bioinformatics Core, City of Hope National Medical Center, Duarte, CA, USA; Department of Molecular Medicine, City of Hope National Medical Center, Duarte, CA, USA; Cancer Immunotherapeutics and Immunology, City of Hope National Medical Center, Duarte, CA, USA; Department of Biology, City of Hope National Medical Center, Duarte, CA, USA; Department of Diabetes and Metabolic Disease Research, City of Hope National Medical Center, Duarte, CA, USA; Functional Genomics Core, City of Hope National Medical Center, Duarte, CA, USA; Department of Molecular & Cellular Biology, City of Hope National Medical Center, Duarte, CA, USA
COHCAP funding source(s)
Supported by The National Institutes of Health [Comprehensive Cancer Center Grant P30 CA33572, R01 CA115674, R01 CA122976] and City of Hope National Medical Center [institutional funding].

COHCAP reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review COHCAP