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Extract read count signals from bam files

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to the bamsignals package HTML R Script
Reference Manual PDF


biocViews Alignment, Coverage, DataImport, Sequencing, Software
Version 1.36.0
In Bioconductor since BioC 3.1 (R-3.2) (9.5 years)
License GPL-2
Depends R (>= 3.5.0)
Imports methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc
System Requirements GNU make
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Suggests testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
Linking To Rcpp, Rhtslib(>= 1.13.1), zlibbioc
Depends On Me
Imports Me AneuFinder, chromstaR, DNAfusion, epigraHMM, karyoploteR, normr, segmenter, hoardeR
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package bamsignals_1.36.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) bamsignals_1.36.0.tgz
macOS Binary (arm64) bamsignals_1.36.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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