appreci8R

This package is for version 3.17 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: 3.17

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 "4.3") 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 1.18.0

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, 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

System Requirements

URL

Suggests GO.db, org.Hs.eg.db

Linking To

Enhances

Depends On Me

Imports Me

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Build Report Build Report

Package Archives

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

Source Package appreci8R_1.18.0.tar.gz

Windows Binary appreci8R_1.18.0.zip

macOS Binary (x86_64) appreci8R_1.18.0.tgz

macOS Binary (arm64) appreci8R_1.18.0.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

Old Source Packages for BioC 3.17 Source Archive