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: 1.6.0
Date: 2016-10-27
Author: Shaohang Xu, Bo Wen
Maintainer: Bo Wen <wenbo@genomics.cn>, Shaohang Xu <xsh.skye@gmail.com>
Depends: R (>= 3.0.1), 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 (>= 1.7.0), pheatmap
Suggests: BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics, BiocStyle,
        knitr, R.utils
VignetteBuilder: knitr
License: GPL-2
biocViews: Proteomics, MassSpectrometry, Software, ReportWriting,
        RNASeq, Sequencing
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-04-25 02:11:33 UTC; biocbuild
Built: R 3.4.0; ; 2017-04-25 15:39:49 UTC; unix
