appreci8R
This package is for version 3.9 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: 3.9
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("appreci8R")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneticVariability, SNP, Sequencing, Software, VariantAnnotation, VariantDetection |
| Version | 1.2.2 |
| 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.ESP6500SI.V2.SSA137.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 |
See More
| Suggests | GO.db, org.Hs.eg.db |
| 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_1.2.2.tar.gz |
| Windows Binary | appreci8R_1.2.2.zip |
| Mac OS X 10.11 (El Capitan) | appreci8R_1.2.2.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 3.9 | Source Archive |