This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see PGA.
Bioconductor version: 3.9
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 (from within R,
enter citation("PGA")
):
To install this package, start R (version "3.6") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("PGA")
For older versions of R, please refer to the appropriate Bioconductor release.
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 |
biocViews | ImmunoOncology, MassSpectrometry, Proteomics, RNASeq, ReportWriting, Sequencing, Software |
Version | 1.14.0 |
In Bioconductor since | BioC 3.2 (R-3.2) (4 years) |
License | GPL-2 |
Depends | R (>= 3.5.0), 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 |
LinkingTo | |
Suggests | RMariaDB, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics, BiocStyle, knitr, R.utils |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | PGA_1.14.0.tar.gz |
Windows Binary | PGA_1.14.0.zip |
Mac OS X 10.11 (El Capitan) | PGA_1.14.0.tgz |
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 |
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