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groHMM specifications


Unique identifier OMICS_07953
Name groHMM
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.14.0
Stability Stable
parallel, GenomeInfoDb, BiocStyle, edgeR, GenomicFeatures, MASS, S4Vectors(>=0.17.25), IRanges(>=2.13.12),, GenomicRanges(>=1.31.8), TxDb.Hsapiens.UCSC.hg19.knownGene, rtracklayer(>=1.39.7), R(>=3.0.2), GenomicAlignments(>=1.15.6)
Maintained Yes


No version available



  • person_outline Minho Chae

Publications for groHMM

groHMM citation


A comprehensive comparison of tools for differential ChIP seq analysis

Brief Bioinform
PMCID: 5142015
PMID: 26764273
DOI: 10.1093/bib/bbv110

[…] false-discovery rate (fdr) or p-value measure, we decided to set the thresholds as fdr ≤ = 0.01 or p-value ≤ = 0.05., we obtained already aligned gro-seq reads for the foxa1 data set as an input for grohmm, which is an r pipeline for the analysis of gro-seq data []. differential gro-seq analysis was performed according to the manual of grohmm using edger with a significance threshold of p ≤ = […]

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groHMM institution(s)
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
groHMM funding source(s)
This work was supported by fellowships from the DOD Breast Cancer Research Program (BC093731) and the American Heart Association. It was also funded by the NIH training award (T32HD052471), a postdoctoral fellowship from the PhRMA Foundation and a grant from the NIH/NIDDK (DK058110).

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