sapFinder
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see sapFinder.
A package for variant peptides detection and visualization in shotgun proteomics.
Bioconductor version: 3.12
sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.
Author: Shaohang Xu, Bo Wen
Maintainer: Shaohang Xu <xsh.skye at gmail.com>, Bo Wen <wenbo at genomics.cn>
citation("sapFinder")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sapFinder")
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("sapFinder")| sapFinder Vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Proteomics, RNASeq, ReportWriting, SNP, Software, Visualization |
| Version | 1.28.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10 years) |
| License | GPL-2 |
| Depends | R (>= 3.0.0), rTANDEM(>= 1.3.5) |
| Imports | pheatmap, Rcpp (>= 0.10.6), graphics, grDevices, stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocGenerics, BiocStyle |
| Linking To | Rcpp |
| 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 | sapFinder_1.28.0.tar.gz |
| Windows Binary | sapFinder_1.28.0.zip (64-bit only) |
| macOS 10.13 (High Sierra) | |
| Source Repository | git clone https://git.bioconductor.org/packages/sapFinder |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sapFinder |
| Package Short Url | https://bioconductor.org/packages/sapFinder/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |