PGA
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 PGA.
An package for identification of novel peptides by customized database derived from RNA-Seq
Bioconductor version: 3.12
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 <wenbostar at gmail.com>, Shaohang Xu <xsh.skye at gmail.com>
citation("PGA")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PGA")
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("PGA")| PGA tutorial | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Proteomics, RNASeq, ReportWriting, Sequencing, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.0.0), 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(>= 1.21.5), pheatmap, dplyr, processx, readr, seqinr |
| System Requirements | |
| URL |
See More
| Suggests | RMariaDB, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics, BiocStyle, knitr, R.utils |
| 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 | PGA_1.20.0.tar.gz |
| Windows Binary | PGA_1.20.0.zip |
| macOS 10.13 (High Sierra) | |
| Source Repository | git clone https://git.bioconductor.org/packages/PGA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PGA |
| Package Short Url | https://bioconductor.org/packages/PGA/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |