appreci8R

DOI: 10.18129/B9.bioc.appreci8R    

This package is for version 3.11 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: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("appreci8R")

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	1.6.0
In Bioconductor since	BioC 3.8 (R-3.5) (2 years)
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.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
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_1.6.0.tar.gz
Windows Binary	appreci8R_1.6.0.zip
macOS 10.13 (High Sierra)	appreci8R_1.6.0.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	https://bioconductor.org/packages/appreci8R/
Package Downloads Report	Download Stats