COHCAP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool COHCAP

Tool usage distribution map

This map represents all the scientific publications referring to COHCAP per scientific context
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Associated diseases


Popular tool citations

chevron_left Differentially methylated region detection Quality control Methylation scoring Differentially methylated region detection Data integration chevron_right
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COHCAP specifications


Unique identifier OMICS_00595
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
RColorBrewer, gplots, Rcpp, WriteXLS, COHCAPanno, RcppArmadillo, BH
Maintained Yes




No version available



Publication for City of Hope CpG Island Analysis Pipeline

COHCAP citations


Use of methylation profiling to identify significant differentially methylated genes in bone marrow mesenchymal stromal cells from acute myeloid leukemia

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

[…] The City of Hope CpG Island Analysis Pipeline (COHCAP) package in Bioconductor ( is an algorithm to analyze either Illumina methylation array or bisulfite sequenci […]


Bioenergetics of acquired cisplatin resistant H1299 non small cell lung cancer and P31 mesothelioma cells

PMCID: 5706906
PMID: 29212260
DOI: 10.18632/oncotarget.21885
call_split See protocol

[…] med 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. […]


Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis

PMCID: 4790440
PMID: 26366945
DOI: 10.2217/epi.15.21

[…] ed for methylation sequencing ratio data. The major advantage of the package is to handle a large dataset through parallel computing and perform a permutation test for multiple testing adjustment []. COHCAP operates on either methylation microarray or bisulfite sequencing data using methylation ratio as input. The package has an option of Fisher's exact test, t-tests and ANOVA []. Attentions are n […]


Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data

PMCID: 4304832
PMID: 25233806
DOI: 10.1016/j.ymeth.2014.08.011

[…] approximately 100 different diseases. This is a powerful tool for integrating smaller datasets to ask different biological questions, to validate results or to observe trends across different samples.COHCAP is a software package that takes methylation data (450k or BS-Seq) that has been preprocessed and identifies CpG islands that show a consistent methylation pattern among CpG sites. This packag […]


Statistical methods for detecting differentially methylated loci and regions

Front Genet
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 moderati […]

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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].

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