recipe bioconductor-appreci8r

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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/appreci8R.html

License

LGPL-3

Recipe

/bioconductor-appreci8r/meta.yaml

package bioconductor-appreci8r

Versions

1.0.0-0

Depends

• bioconductor-biostrings >=2.50.0,<2.51.0

• bioconductor-bsgenome >=1.50.0,<1.51.0

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

• bioconductor-cosmic.67 >=1.18.0,<1.19.0

• bioconductor-genomicfeatures >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-genomicscores >=1.6.0,<1.7.0

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

• bioconductor-iranges >=2.16.0,<2.17.0

• bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.7.0,<3.8.0

• bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5 >=3.7.0,<3.8.0

• bioconductor-mafdb.exac.r1.0.hs37d5 >=3.7.0,<3.8.0

• bioconductor-mafdb.gnomadex.r2.0.1.hs37d5 >=3.8.0,<3.9.0

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

• bioconductor-rsamtools >=1.34.0,<1.35.0

• bioconductor-s4vectors >=0.20.0,<0.21.0

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

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

• bioconductor-summarizedexperiment >=1.12.0,<1.13.0

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

• bioconductor-variantannotation >=1.28.0,<1.29.0

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

• r-base >=3.5.1,<3.5.2.0a0

• 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)