bamsignals

DOI: 10.18129/B9.bioc.bamsignals    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see bamsignals.

Extract read count signals from bam files

Bioconductor version: 3.12

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: Johannes Helmuth <johannes.helmuth at laborberlin.com>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("bamsignals")

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("bamsignals")

 

HTML R Script Introduction to the bamsignals package
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, Coverage, DataImport, Sequencing, Software
Version 1.22.0
In Bioconductor since BioC 3.1 (R-3.2) (6 years)
License GPL-2
Depends R (>= 3.2.0)
Imports methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc
LinkingTo Rcpp, Rhtslib(>= 1.13.1), zlibbioc
Suggests testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
SystemRequirements GNU make
Enhances
URL https://github.com/lamortenera/bamsignals
BugReports https://github.com/lamortenera/bamsignals/issues
Depends On Me
Imports Me AneuFinder, chromstaR, karyoploteR, normr
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package bamsignals_1.22.0.tar.gz
Windows Binary bamsignals_1.22.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) bamsignals_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/bamsignals
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bamsignals
Package Short Url https://bioconductor.org/packages/bamsignals/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: