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bamsignals

Extract read count signals from bam files


Bioconductor version: Release (3.18)

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 "4.3") 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")
Introduction to the bamsignals package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, Coverage, DataImport, Sequencing, Software
Version 1.34.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License GPL-2
Depends R (>= 3.5.0)
Imports methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc
System Requirements GNU make
URL https://github.com/lamortenera/bamsignals
Bug Reports https://github.com/lamortenera/bamsignals/issues
See More
Suggests testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
Linking To Rcpp, Rhtslib(>= 1.13.1), zlibbioc
Enhances
Depends On Me
Imports Me AneuFinder, chromstaR, DNAfusion, epigraHMM, karyoploteR, normr, segmenter
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package bamsignals_1.34.0.tar.gz
Windows Binary bamsignals_1.34.0.zip (64-bit only)
macOS Binary (x86_64) bamsignals_1.34.0.tgz
macOS Binary (arm64) bamsignals_1.34.0.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