bamsignals
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 laborberlin.com>
Citation (from within R, enter
citation("bamsignals")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| 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 |
| 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, DNAfusion, chromstaR, epigraHMM, karyoploteR, normr, segmenter, hoardeR |
| 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_1.36.0.tar.gz |
| Windows Binary (x86_64) | bamsignals_1.36.0.zip (64-bit only) |
| macOS Binary (x86_64) | bamsignals_1.36.0.tgz |
| macOS Binary (arm64) | bamsignals_1.36.0.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 |