DOI: 10.18129/B9.bioc.appreci8R  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see appreci8R.

appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV

Bioconductor version: 3.16

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.

Author: Sarah Sandmann

Maintainer: Sarah Sandmann <sarah.sandmann at>

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biocViews GeneticVariability, SNP, Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.16.0
In Bioconductor since BioC 3.8 (R-3.5) (4.5 years)
License LGPL-3
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, rsnps, 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, utils, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment
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