appreci8R

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

Bioconductor version: Release (3.19)

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 "4.4") and enter:


if (!require("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")

Using appreci8R	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneticVariability, SNP, Sequencing, Software, VariantAnnotation, VariantDetection
Version	1.22.0
In Bioconductor since	BioC 3.8 (R-3.5) (6 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, 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
System Requirements
URL

Suggests	GO.db, org.Hs.eg.db, utils
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	appreci8R_1.22.0.tar.gz
Windows Binary (x86_64)	appreci8R_1.22.0.zip
macOS Binary (x86_64)	appreci8R_1.22.0.tgz
macOS Binary (arm64)	appreci8R_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/appreci8R
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/appreci8R
Bioc Package Browser	https://code.bioconductor.org/browse/appreci8R/
Package Short Url	https://bioconductor.org/packages/appreci8R/
Package Downloads Report	Download Stats