appreci8R

DOI: 10.18129/B9.bioc.appreci8R    

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

Bioconductor version: Release (3.8)

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 uni-muenster.de>

Citation (from within R, enter citation("appreci8R")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("appreci8R", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("appreci8R")

 

PDF R Script Using appreci8R
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneticVariability, SNP, Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.0.0
License LGPL-3
Depends
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.ESP6500SI.V2.SSA137.hs37d5, MafDb.gnomADex.r2.0.1.hs37d5, COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr, utils, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment
LinkingTo
Suggests GO.db, org.Hs.eg.db
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package appreci8R_1.0.0.tar.gz
Windows Binary appreci8R_1.0.0.zip
Mac OS X 10.11 (El Capitan) appreci8R_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/appreci8R
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/appreci8R
Package Short Url http://bioconductor.org/packages/appreci8R/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: