proBAMr

This is the released version of proBAMr; for the devel version, see proBAMr.

Generating SAM file for PSMs in shotgun proteomics data

Bioconductor version: Release (3.21)

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>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("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")

Introduction to proBAMr	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, Software, Visualization
Version	1.42.0
In Bioconductor since	BioC 3.0 (R-3.1) (11 years)
License	Artistic-2.0
Depends	R (>= 3.0.1), IRanges, AnnotationDbi
Imports	GenomicRanges, Biostrings, GenomicFeatures, txdbmaker, rtracklayer
System Requirements
URL

Suggests	RUnit, BiocGenerics
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	proBAMr_1.42.0.tar.gz
Windows Binary (x86_64)	proBAMr_1.42.0.zip
macOS Binary (x86_64)	proBAMr_1.42.0.tgz
macOS Binary (arm64)	proBAMr_1.42.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/proBAMr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/proBAMr
Bioc Package Browser	https://code.bioconductor.org/browse/proBAMr/
Package Short Url	https://bioconductor.org/packages/proBAMr/
Package Downloads Report	Download Stats