recipe bioconductor-appreci8r

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

Homepage

https://bioconductor.org/packages/3.12/bioc/html/appreci8R.html

License

LGPL-3

Recipe

/bioconductor-appreci8r/meta.yaml

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.

package bioconductor-appreci8r

Versions

1.8.0-1,  1.6.0-0,  1.4.0-1,  1.0.0-0

Depends

• bioconductor-biostrings >=2.58.0,<2.59.0

• bioconductor-bsgenome >=1.58.0,<1.59.0

• bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0

• bioconductor-cosmic.67 >=1.26.0,<1.27.0

• bioconductor-genomicfeatures >=1.42.0,<1.43.0

• bioconductor-genomicranges >=1.42.0,<1.43.0

• bioconductor-genomicscores >=2.2.0,<2.3.0

• bioconductor-homo.sapiens >=1.3.0,<1.4.0

• bioconductor-iranges >=2.24.0,<2.25.0

• bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.10.0,<3.11.0

• bioconductor-mafdb.exac.r1.0.hs37d5 >=3.10.0,<3.11.0

• bioconductor-mafdb.gnomadex.r2.1.hs37d5 >=3.10.0,<3.11.0

• bioconductor-polyphen.hsapiens.dbsnp131 >=1.0.0,<1.1.0

• bioconductor-rsamtools >=2.6.0,<2.7.0

• bioconductor-s4vectors >=0.28.0,<0.29.0

• bioconductor-sift.hsapiens.dbsnp137 >=1.0.0,<1.1.0

• bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0

• bioconductor-summarizedexperiment >=1.20.0,<1.21.0

• bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0

• bioconductor-variantannotation >=1.36.0,<1.37.0

• bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0

• r-base >=4.0,<4.1.0a0

• r-dt

• r-openxlsx

• r-rentrez

• r-rsnps

• r-seqinr

• r-shiny

• r-shinyjs

• r-stringr

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-appreci8r

and update with:

conda update bioconductor-appreci8r

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-appreci8r:<tag>

(see bioconductor-appreci8r/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-appreci8r/README.html)