recipe r-flanders

Fast colocalization using AnnData objects in R

Homepage:

https://github.com/Biostatistics-Unit-HT/flanders_r

License:

MIT / MIT

Recipe:

/r-flanders/meta.yaml

flanders is an R package designed to seamlessly convert finemapping output files from the nf-flanders pipeline into a unified AnnData object and facilitate colocalization analysis. The package provides functions to: - Convert multiple *finemap.rds files into a single AnnData object with credible set metadata. - Generate an input table (coloc_input) for colocalization testing. - Run pairwise colocalization tests, with minimal runtime overhead (typically 5–10 tests per second on standard hardware).

package r-flanders

versions:

1.0.0-0

depends bioconductor-scrnaseq:

depends bioconductor-singlecellexperiment:

depends bioconductor-zellkonverter:

depends r-anndata:

depends r-base:

>=4.4,<4.5.0a0

depends r-coloc:

depends r-data.table:

depends r-dplyr:

depends r-matrix:

depends r-optparse:

depends r-susier:

requirements:

additional platforms:

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 r-flanders

and update with::

   mamba update r-flanders

To create a new environment, run:

mamba create --name myenvname r-flanders

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/r-flanders:<tag>

(see `r-flanders/tags`_ for valid values for ``<tag>``)

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