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

(downloads) docker_bioconductor-appreci8r

Versions

1.0.0-0

Depends bioconductor-biostrings

>=2.50.0,<2.51.0

Depends bioconductor-bsgenome

>=1.50.0,<1.51.0

Depends bioconductor-bsgenome.hsapiens.ucsc.hg19

>=1.4.0,<1.5.0

Depends bioconductor-cosmic.67

>=1.18.0,<1.19.0

Depends bioconductor-genomicfeatures

>=1.34.0,<1.35.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-genomicscores

>=1.6.0,<1.7.0

Depends bioconductor-homo.sapiens

>=1.3.0,<1.4.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-mafdb.1kgenomes.phase3.hs37d5

>=3.7.0,<3.8.0

Depends bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5

>=3.7.0,<3.8.0

Depends bioconductor-mafdb.exac.r1.0.hs37d5

>=3.7.0,<3.8.0

Depends bioconductor-mafdb.gnomadex.r2.0.1.hs37d5

>=3.8.0,<3.9.0

Depends bioconductor-polyphen.hsapiens.dbsnp131

>=1.0.0,<1.1.0

Depends bioconductor-rsamtools

>=1.34.0,<1.35.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-sift.hsapiens.dbsnp137

>=1.0.0,<1.1.0

Depends bioconductor-snplocs.hsapiens.dbsnp144.grch37

>=0.99.0,<0.100.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene

>=3.2.0,<3.3.0

Depends bioconductor-variantannotation

>=1.28.0,<1.29.0

Depends bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37

>=0.99.0,<0.100.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-dt

Depends r-openxlsx

Depends r-rentrez

Depends r-rsnps

Depends r-seqinr

Depends r-shiny

Depends r-shinyjs

Depends r-stringr

Requirements

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>)