recipe bioconductor-mungesumstats

Standardise summary statistics from GWAS

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/MungeSumstats.html

License:

Artistic-2.0

Recipe:

/bioconductor-mungesumstats/meta.yaml

The *MungeSumstats* package is designed to facilitate the standardisation of GWAS summary statistics. It reformats inputted summary statisitics to include SNP, CHR, BP and can look up these values if any are missing. It also pefrorms dozens of QC and filtering steps to ensure high data quality and minimise inter-study differences.

package bioconductor-mungesumstats

versions:

1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-bsgenome:

>=1.68.0,<1.69.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends bioconductor-variantannotation:

>=1.46.0,<1.47.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-googleauthr:

depends r-httr:

depends r-jsonlite:

depends r-magrittr:

depends r-r.utils:

depends r-rcurl:

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-mungesumstats

and update with::

   mamba update bioconductor-mungesumstats

To create a new environment, run:

mamba create --name myenvname bioconductor-mungesumstats

with myenvname being 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-mungesumstats:<tag>

(see `bioconductor-mungesumstats/tags`_ for valid values for ``<tag>``)

Download stats

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-mungesumstats/README.html)