groHMM

This is the development version of groHMM; for the stable release version, see groHMM.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0

GRO-seq Analysis Pipeline

Bioconductor version: Development (3.24)

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: 0000-0001-9726-4552

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

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

Charles G. Danko, Minho Chae, W. Lee Kraus. groHMM: GRO-seq Analysis Pipeline. doi:10.18129/B9.bioc.groHMM, R package version 1.47.0, https://bioconductor.org/packages/groHMM.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	1.47.0
In Bioconductor since	BioC 3.0 (R-3.1) (12 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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	groHMM_1.47.0.tar.gz
Windows Binary (x86_64)	groHMM_1.47.0.zip
macOS Binary (big-sur-x86_64)	groHMM_1.47.0.tgz
macOS Binary (sonoma-arm64)	groHMM_1.47.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/groHMM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/groHMM
Package Short Url	https://bioconductor.org/packages/groHMM/
Package Downloads Report	Download Stats