Package: PGA
Type: Package
Title: An package for identification of novel peptides by customized
        database derived from RNA-Seq
Description: 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.
Version: 1.20.0
Date: 2020-08-26
Author: Shaohang Xu, Bo Wen
Maintainer: Bo Wen <wenbostar@gmail.com>, Shaohang Xu <xsh.skye@gmail.com>
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
VignetteBuilder: knitr
License: GPL-2
biocViews: Proteomics, ImmunoOncology, MassSpectrometry, Software,
        ReportWriting, RNASeq, Sequencing
NeedsCompilation: no
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/PGA
git_branch: RELEASE_3_12
git_last_commit: 4e7418a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-27
Packaged: 2020-10-28 03:30:24 UTC; biocbuild
Built: R 4.0.3; ; 2020-10-28 14:55:03 UTC; windows
