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 (3.23)
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("proBAMr")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Proteomics, Software, Visualization |
| Version | 1.46.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0.1), IRanges, AnnotationDbi |
| Imports | GenomicRanges, Biostrings, GenomicFeatures, txdbmaker, rtracklayer |
| System Requirements | |
| URL |
See More
| Suggests | GenomeInfoDbData, 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_1.46.0.tar.gz |
| Windows Binary (x86_64) | proBAMr_1.46.0.zip |
| macOS Binary (big-sur-x86_64) | proBAMr_1.46.0.tgz |
| macOS Binary (sonoma-arm64) | proBAMr_1.46.0.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 |