Package: appreci8R
Type: Package
Title: appreci8R: an R/Bioconductor package for filtering SNVs and
        short indels with high sensitivity and high PPV
Version: 1.24.0
Author: Sarah Sandmann
Maintainer: Sarah Sandmann <sarah.sandmann@uni-muenster.de>
Description: The appreci8R is an R version of our appreci8-algorithm - A Pipeline for
    PREcise variant Calling Integrating 8 tools. Variant calling results of our 
    standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer,
    samtools and VarDict), as well as up to 5 additional tools is combined, evaluated
    and filtered.
License: LGPL-3
Encoding: UTF-8
Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome,
        BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
        Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37,
        XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, Biostrings,
        MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5,
        MafDb.gnomADex.r2.1.hs37d5, COSMIC.67, rentrez,
        PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137, seqinr,
        openxlsx, Rsamtools, stringr, stats, GenomicRanges, S4Vectors,
        GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment
Suggests: GO.db, org.Hs.eg.db, utils
biocViews: VariantDetection, GeneticVariability, SNP,
        VariantAnnotation, Sequencing,
RoxygenNote: 6.0.1
git_url: https://git.bioconductor.org/packages/appreci8R
git_branch: RELEASE_3_20
git_last_commit: 8bc7a20
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
NeedsCompilation: no
Packaged: 2024-10-30 01:10:22 UTC; biocbuild
Built: R 4.4.1; ; 2024-10-30 15:25:36 UTC; windows
