proBAMr

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

Generating SAM file for PSMs in shotgun proteomics data

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DOI: 10.18129/B9.bioc.proBAMr

Bioconductor version: Development (3.23)

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 "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software, Visualization

Version 1.45.0

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 GenomeInfoDbData, RUnit, BiocGenerics

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Package Archives

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

Source Package proBAMr_1.45.0.tar.gz

Windows Binary (x86_64) proBAMr_1.45.0.zip

macOS Binary (x86_64)

macOS Binary (arm64)

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/

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