DESCRIPTION

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: 1.15.4
Date: 2020-09-01
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