- Home
- Bioconductor 3.0
- Software Packages
- bumphunter
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("bumphunter")
In most cases, you don't need to download the package archive at all.
bumphunter
Bump Hunter
Bioconductor version: 3.0
Tools for finding bumps in genomic data
Author: Rafael A. Irizarry [cre, aut], Martin Ayree [aut], Kasper Daniel Hansen [aut], Hector Corrada Hansen [aut], Shan Andrews [ctb], Andrew E. Jaffe [ctb], Harris Jaffee [ctb]
Maintainer: Rafael A. Irizarry <rafa at jimmy.harvard.edu>
Citation (from within R,
enter citation("bumphunter")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("bumphunter")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("bumphunter")
| R Script | The bumphunter user's guide | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DNAMethylation, Epigenetics, Infrastructure, MultipleComparison, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, foreach, iterators, methods, parallel, locfit |
| Imports | matrixStats, limma, doRNG, BiocGenerics, utils |
| LinkingTo | |
| Suggests | RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/ririzarr/bumphunter |
| Depends On Me | minfi |
| Imports Me | derfinder |
| Suggests Me | derfinderPlot |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | bumphunter_1.6.0.tar.gz |
| Windows Binary | bumphunter_1.6.0.zip |
| Mac OS X 10.6 (Snow Leopard) | bumphunter_1.6.0.tgz |
| Mac OS X 10.9 (Mavericks) | bumphunter_1.6.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2015, Bioconductor
