bamsignals

DOI: 10.18129/B9.bioc.bamsignals  

Extract read count signals from bam files

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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	1.30.0
In Bioconductor since	BioC 3.1 (R-3.2) (8 years)
License	GPL-2
Depends	R (>= 3.5.0)
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, DNAfusion, epigraHMM, karyoploteR, normr, segmenter
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	bamsignals_1.30.0.tar.gz
Windows Binary	bamsignals_1.30.0.zip (64-bit only)
macOS Binary (x86_64)	bamsignals_1.30.0.tgz
macOS Binary (arm64)	bamsignals_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/bamsignals
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/bamsignals
Bioc Package Browser	https://code.bioconductor.org/browse/bamsignals/
Package Short Url	https://bioconductor.org/packages/bamsignals/
Package Downloads Report	Download Stats