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/3.13/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

1.10.0-0,  1.8.0-1,  1.6.0-0,  1.4.0-1,  1.0.0-0

Depends

• bioconductor-biostrings >=2.60.0,<2.61.0

• bioconductor-bsgenome >=1.60.0,<1.61.0

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

• bioconductor-cosmic.67 >=1.28.0,<1.29.0

• bioconductor-genomicfeatures >=1.44.0,<1.45.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-genomicscores >=2.4.0,<2.5.0

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

• bioconductor-iranges >=2.26.0,<2.27.0

• 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 >=2.8.0,<2.9.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

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

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

• bioconductor-summarizedexperiment >=1.22.0,<1.23.0

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

• bioconductor-variantannotation >=1.38.0,<1.39.0

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

• r-base >=4.1,<4.2.0a0

• 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>)

Download stats

Link to this page

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