bumphunter

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see bumphunter.

Bump Hunter

Bioconductor version: 3.18

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")):

Installation

To install this package, start R (version "4.3") 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 1.44.0

In Bioconductor since BioC 2.12 (R-3.0) (11 years)

License Artistic-2.0

Depends R (>= 3.5), S4Vectors(>= 0.9.25), IRanges(>= 2.3.23), GenomeInfoDb, 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, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene

Linking To

Enhances

Depends On Me minfi

Imports Me brainflowprobes, ChAMP, coMethDMR, DAMEfinder, derfinder, dmrseq, epimutacions, epivizr, GenomicState, methylCC, recountWorkflow, rnaEditr

Suggests Me bigmelon, derfinderPlot, epivizrData, regionReport

Links To Me

Build Report Build Report

Package Archives

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

Source Package bumphunter_1.44.0.tar.gz

Windows Binary bumphunter_1.44.0.zip

macOS Binary (x86_64) bumphunter_1.44.0.tgz

macOS Binary (arm64) bumphunter_1.44.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/bumphunter

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bumphunter

Bioc Package Browser https://code.bioconductor.org/browse/bumphunter/

Package Short Url https://bioconductor.org/packages/bumphunter/

Package Downloads Report Download Stats