bumphunter

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

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, 2.14, 2.13, 2.12

Bump Hunter

Bioconductor version: Release (3.23)

Tools for finding bumps in genomic data

Author: Rafael A. Irizarry [aut], Martin Aryee [aut], Kasper Daniel Hansen [aut], Hector Corrada Bravo [aut], Shan Andrews [ctb], Andrew E. Jaffe [ctb], Harris Jaffee [ctb], Leonardo Collado-Torres [ctb], Tamilselvi Guharaj [cre]

Maintainer: Tamilselvi Guharaj <selvi at ds.dfci.harvard.edu>

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

Rafael A. Irizarry, Martin Aryee, Kasper Daniel Hansen, Hector Corrada Bravo. bumphunter: Bump Hunter. doi:10.18129/B9.bioc.bumphunter, R package version 1.54.0, https://bioconductor.org/packages/bumphunter.

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")

BiocManager::install("bumphunter")

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("bumphunter")

The bumphunter user's guide	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, Epigenetics, ImmunoOncology, Infrastructure, MultipleComparison, Software
Version	1.54.0
In Bioconductor since	BioC 2.12 (R-3.0) (13.5 years)
License	Artistic-2.0
Depends	R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), Seqinfo, GenomicRanges, foreach, iterators, methods, parallel, locfit
Imports	matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats
System Requirements
URL	https://github.com/rafalab/bumphunter

Suggests	testthat, RUnit, doParallel, GenomeInfoDb, txdbmaker, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene
Linking To
Enhances
Depends On Me	minfi
Imports Me	ChAMP, coMethDMR, DAMEfinder, derfinder, dmrseq, epimutacions, epivizr, GenomicState, methylCC, recountWorkflow, rnaEditr, vmrseq
Suggests Me	bigmelon, derfinderPlot, epivizrData, regionReport
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	bumphunter_1.54.0.tar.gz
Windows Binary (x86_64)	bumphunter_1.54.0.zip
macOS Binary (big-sur-x86_64)	bumphunter_1.54.0.tgz
macOS Binary (sonoma-arm64)	bumphunter_1.54.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/bumphunter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/bumphunter
Package Short Url	https://bioconductor.org/packages/bumphunter/
Package Downloads Report	Download Stats