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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("bamsignals")
In most cases, you don't need to download the package archive at all.
bamsignals
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see bamsignals.
Extract read count signals from bam files
Bioconductor version: 3.4
This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.
Author: Alessandro Mammana [aut, cre], Johannes Helmuth [aut]
Maintainer: Alessandro Mammana <mammana at molgen.mpg.de>
Citation (from within R,
enter citation("bamsignals")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("bamsignals")
Documentation
| HTML | R Script | Introduction to the bamsignals package |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, Coverage, DataImport, Sequencing, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (2 years) |
| License | GPL-2 |
| Depends | R (>= 3.2.0) |
| Imports | methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc |
| LinkingTo | Rcpp, Rhtslib, zlibbioc |
| Suggests | testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | AneuFinder, chromstaR, normr |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | bamsignals_1.6.0.tar.gz |
| Windows Binary | bamsignals_1.6.0.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | bamsignals_1.6.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/bamsignals/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/bamsignals/ |
| Package Downloads Report | Download Stats |
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