- 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/3.14/bioc/html/appreci8R.html
- License:
LGPL-3
- Recipe:
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:
1.12.0-0
,1.10.0-0
,1.8.0-1
,1.6.0-0
,1.4.0-1
,1.0.0-0
- Depends:
bioconductor-biostrings
>=2.62.0,<2.63.0
bioconductor-bsgenome
>=1.62.0,<1.63.0
bioconductor-bsgenome.hsapiens.ucsc.hg19
>=1.4.0,<1.5.0
bioconductor-cosmic.67
>=1.30.0,<1.31.0
bioconductor-genomicfeatures
>=1.46.0,<1.47.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-genomicscores
>=2.6.0,<2.7.0
bioconductor-homo.sapiens
>=1.3.0,<1.4.0
bioconductor-iranges
>=2.28.0,<2.29.0
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
>=2.10.0,<2.11.0
bioconductor-s4vectors
>=0.32.0,<0.33.0
bioconductor-sift.hsapiens.dbsnp137
>=1.0.0,<1.1.0
bioconductor-snplocs.hsapiens.dbsnp144.grch37
>=0.99.0,<0.100.0
bioconductor-summarizedexperiment
>=1.24.0,<1.25.0
bioconductor-txdb.hsapiens.ucsc.hg19.knowngene
>=3.2.0,<3.3.0
bioconductor-variantannotation
>=1.40.0,<1.41.0
bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37
>=0.99.0,<0.100.0
r-base
>=4.1,<4.2.0a0
- Required By:
Installation
With an activated Bioconda channel (see 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¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-appreci8r/README.html)