groHMM statistics

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Citations per year

Number of citations per year for the bioinformatics software tool groHMM
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groHMM specifications

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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
Requirements
parallel, GenomeInfoDb, BiocStyle, edgeR, GenomicFeatures, MASS, S4Vectors(>=0.17.25), IRanges(>=2.13.12), org.Hs.eg.db, GenomicRanges(>=1.31.8), TxDb.Hsapiens.UCSC.hg19.knownGene, rtracklayer(>=1.39.7), R(>=3.0.2), GenomicAlignments(>=1.15.6)
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Minho Chae

Publications for groHMM

groHMM citation

library_books

A comprehensive comparison of tools for differential ChIP seq analysis

2016
Brief Bioinform
PMCID: 5142015
PMID: 26764273
DOI: 10.1093/bib/bbv110

[…] 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 ≤ = 0.0 […]


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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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