- 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/3.17/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:
1.16.0-0,1.12.0-0,1.10.0-0,1.8.0-1,1.6.0-0,1.4.0-1,1.0.0-0- depends bioconductor-biostrings:
>=2.66.0,<2.67.0- depends bioconductor-bsgenome:
>=1.66.0,<1.67.0- depends bioconductor-bsgenome.hsapiens.ucsc.hg19:
>=1.4.0,<1.5.0- depends bioconductor-cosmic.67:
>=1.34.0,<1.35.0- depends bioconductor-genomicfeatures:
>=1.50.0,<1.51.0- depends bioconductor-genomicranges:
>=1.50.0,<1.51.0- depends bioconductor-genomicscores:
>=2.10.0,<2.11.0- depends bioconductor-homo.sapiens:
>=1.3.0,<1.4.0- depends bioconductor-iranges:
>=2.32.0,<2.33.0- depends bioconductor-mafdb.1kgenomes.phase3.hs37d5:
>=3.10.0,<3.11.0- depends bioconductor-mafdb.exac.r1.0.hs37d5:
>=3.10.0,<3.11.0- depends bioconductor-mafdb.gnomadex.r2.1.hs37d5:
>=3.10.0,<3.11.0- depends bioconductor-polyphen.hsapiens.dbsnp131:
>=1.0.0,<1.1.0- depends bioconductor-rsamtools:
>=2.14.0,<2.15.0- depends bioconductor-s4vectors:
>=0.36.0,<0.37.0- 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:
>=1.28.0,<1.29.0- depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:
>=3.2.0,<3.3.0- depends bioconductor-variantannotation:
>=1.44.0,<1.45.0- depends bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37:
>=0.99.0,<0.100.0- depends r-base:
>=4.2,<4.3.0a0- 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
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-appreci8r and update with:: mamba update bioconductor-appreci8r
To create a new environment, run:
mamba create --name myenvname bioconductor-appreci8r
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, 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)
