groHMM

This is the released version of groHMM; for the devel version, see groHMM.

GRO-seq Analysis Pipeline

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DOI: 10.18129/B9.bioc.groHMM

Bioconductor version: Release (3.22)

A pipeline for the analysis of GRO-seq data.

Author: Charles G. Danko [aut], Minho Chae [aut], Andre Martins [ctb], W. Lee Kraus [aut, fnd], Anusha Nagari [ctb], Tulip Nandu [cre, ctb], Pariksheet Nanda [ctb] ORCID iD ORCID: 0000-0001-9726-4552

Maintainer: Tulip Nandu <tulip.nandu at utsouthwestern.edu>

Citation (from within R, enter citation("groHMM")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("groHMM")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("groHMM")

groHMM tutorial PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Sequencing, Software

Version 1.44.0

In Bioconductor since BioC 3.0 (R-3.1) (11 years)

License GPL-3

Depends R (>= 4.1.0), MASS, parallel, S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), Seqinfo, GenomicRanges(>= 1.31.8), GenomicAlignments(>= 1.15.6), rtracklayer(>= 1.39.7)

Imports

System Requirements

URL https://github.com/Kraus-Lab/groHMM

Bug Reports https://github.com/Kraus-Lab/groHMM/issues

Suggests BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene

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