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proBAMr

This is the development version of proBAMr; for the stable release version, see proBAMr.

Generating SAM file for PSMs in shotgun proteomics data


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software, Visualization
Version 1.37.1
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License Artistic-2.0
Depends R (>= 3.0.1), IRanges, AnnotationDbi
Imports GenomicRanges, Biostrings, GenomicFeatures, txdbmaker, rtracklayer
System Requirements
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Suggests RUnit, BiocGenerics
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Package Archives

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

Source Package proBAMr_1.37.1.tar.gz
Windows Binary proBAMr_1.37.1.zip
macOS Binary (x86_64) proBAMr_1.37.1.tgz
macOS Binary (arm64) proBAMr_1.37.1.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