DOI: 10.18129/B9.bioc.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>, Shaohang Xu <xsh.skye at>

Citation (from within R, enter citation("PGA")):


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if (!requireNamespace("BiocManager", quietly = TRUE))


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PDF R Script PGA tutorial
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biocViews ImmunoOncology, MassSpectrometry, Proteomics, RNASeq, ReportWriting, Sequencing, Software
Version 1.20.0
In Bioconductor since BioC 3.2 (R-3.2) (5.5 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
Suggests RMariaDB, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics, BiocStyle, knitr, R.utils
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package PGA_1.20.0.tar.gz
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