bumphunter
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see bumphunter.
Bump Hunter
Bioconductor version: 3.10
Tools for finding bumps in genomic data
Author: Rafael A. Irizarry [cre, 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]
Maintainer: Rafael A. Irizarry <rafa at jimmy.harvard.edu>
citation("bumphunter")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Epigenetics, ImmunoOncology, Infrastructure, MultipleComparison, Software |
| Version | 1.28.0 |
| 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/ririzarr/bumphunter |
See More
| Suggests | testthat, RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene |
| Linking To | |
| Enhances | |
| Depends On Me | minfi |
| Imports Me | brainflowprobes, ChAMP, derfinder, dmrseq, GenomicState, methylCC, methyvim, recountWorkflow |
| 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_1.28.0.tar.gz |
| Windows Binary | bumphunter_1.28.0.zip |
| Mac OS X 10.11 (El Capitan) | bumphunter_1.28.0.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 |
| Old Source Packages for BioC 3.10 | Source Archive |