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appreci8R

This is the development version of appreci8R; for the stable release version, see appreci8R.

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


Bioconductor version: Development (3.20)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews GeneticVariability, SNP, Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.23.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 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
See More
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_1.23.0.tar.gz
Windows Binary appreci8R_1.23.0.zip
macOS Binary (x86_64) appreci8R_1.23.0.tgz
macOS Binary (arm64) appreci8R_1.23.0.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