To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PGA")
In most cases, you don't need to download the package archive at all.
PGA
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An package for identification of novel peptides by customized database derived from RNA-Seq
Bioconductor version: Release (3.4)
This package provides functions for construction of customized protein databases based on RNA-Seq data with/without genome guided, database searching, post-processing and report generation. This kind of customized protein database includes both the reference database (such as Refseq or ENSEMBL) and the novel peptide sequences form RNA-Seq data.
Author: Shaohang Xu, Bo Wen
Maintainer: Bo Wen <wenbo at genomics.cn>, Shaohang Xu <xsh.skye at gmail.com>
Citation (from within R,
enter citation("PGA")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PGA")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PGA")
| R Script | PGA tutorial | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | MassSpectrometry, Proteomics, RNASeq, ReportWriting, Sequencing, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (1.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.0.1), IRanges, GenomicRanges, Biostrings(>= 2.26.3), data.table, rTANDEM |
| Imports | S4Vectors(>= 0.9.25), Rsamtools(>= 1.10.2), GenomicFeatures(>= 1.19.8), biomaRt(>= 2.17.1), stringr, RCurl, Nozzle.R1, VariantAnnotation(>= 1.7.28), rtracklayer, RSQLite, ggplot2, AnnotationDbi, customProDB(>= 1.7.0), pheatmap |
| LinkingTo | |
| Suggests | BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics, BiocStyle, knitr, R.utils |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | PGA_1.4.0.tar.gz |
| Windows Binary | PGA_1.4.0.zip |
| Mac OS X 10.9 (Mavericks) | PGA_1.4.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/PGA/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/PGA/ |
| Package Downloads Report | Download Stats |
Documentation »
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