proBAMr

DOI: 10.18129/B9.bioc.proBAMr    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see proBAMr.

Generating SAM file for PSMs in shotgun proteomics data

Bioconductor version: 3.9

Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file.

Author: Xiaojing Wang

Maintainer: Xiaojing Wang <xiaojing.wang at vanderbilt.edu>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("proBAMr")

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("proBAMr")

 

PDF	R Script	Introduction to proBAMr
PDF		Reference Manual
Text		NEWS

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, Software, Visualization
Version	1.18.0
In Bioconductor since	BioC 3.0 (R-3.1) (5 years)
License	Artistic-2.0
Depends	R (>= 3.0.1), IRanges, AnnotationDbi
Imports	GenomicRanges, Biostrings, GenomicFeatures, rtracklayer
LinkingTo
Suggests	RUnit, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	proBAMr_1.18.0.tar.gz
Windows Binary	proBAMr_1.18.0.zip
Mac OS X 10.11 (El Capitan)	proBAMr_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/proBAMr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/proBAMr
Package Short Url	https://bioconductor.org/packages/proBAMr/
Package Downloads Report	Download Stats