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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("sapFinder")
In most cases, you don't need to download the package archive at all.
sapFinder
A package for variant peptides detection and visualization in shotgun proteomics.
Bioconductor version: 2.14
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 (from within R,
enter citation("sapFinder")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("sapFinder")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("sapFinder")
| R Script | sapFinder Vignette | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | MassSpectrometry, Proteomics, RNASeq, ReportWriting, SNP, Software, Visualization |
| Version | 1.0.1 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | GPL-2 |
| Depends | R (>= 3.0.0), rTANDEM(>= 1.3.5) |
| Imports | pheatmap, Rcpp (>= 0.10.6), graphics, grDevices, stats, utils |
| Suggests | RUnit, BiocGenerics, BiocStyle |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | sapFinder_1.0.1.tar.gz |
| Windows Binary | sapFinder_1.0.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | sapFinder_1.0.1.tgz |
| Mac OS X 10.9 (Mavericks) | sapFinder_1.0.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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