bamsignals

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see bamsignals.

Extract read count signals from bam files

Bioconductor version: 3.17

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Coverage, DataImport, Sequencing, Software

Version 1.32.0

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

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_1.32.0.tar.gz

Windows Binary bamsignals_1.32.0.zip (64-bit only)

macOS Binary (x86_64) bamsignals_1.32.0.tgz

macOS Binary (arm64) bamsignals_1.32.0.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

Old Source Packages for BioC 3.17 Source Archive