bamsignals

This is the development version of bamsignals; for the stable release version, see bamsignals.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1

Extract read count signals from bam files

Bioconductor version: Development (3.24)

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")):

Alessandro Mammana, Johannes Helmuth. bamsignals: Extract read count signals from bam files. doi:10.18129/B9.bioc.bamsignals, R package version 1.45.1, https://bioconductor.org/packages/bamsignals.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Coverage, DataImport, Sequencing, Software
Version	1.45.1
In Bioconductor since	BioC 3.1 (R-3.2) (11.5 years)
License	GPL-2
Depends	R (>= 3.5.0)
Imports	methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges
System Requirements	GNU make
URL	https://github.com/lamortenera/bamsignals
Bug Reports	https://github.com/lamortenera/bamsignals/issues

Suggests	testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
Linking To	Rcpp, Rhtslib (>= 1.13.1)
Enhances
Depends On Me
Imports Me	crupR, fourSynergy, karyoploteR, normr, segmenter
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	bamsignals_1.45.1.tar.gz
Windows Binary (x86_64)	bamsignals_1.45.1.zip (64-bit only)
macOS Binary (big-sur-x86_64)	bamsignals_1.45.1.tgz
macOS Binary (sonoma-arm64)	bamsignals_1.45.1.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