- recipe r-flanders
Fast colocalization using AnnData objects in R
- Homepage:
- License:
MIT / MIT
- Recipe:
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:
1.0.1-0,1.0.0-0- Depends:
on bioconductor-scrnaseq
on bioconductor-singlecellexperiment
on bioconductor-zellkonverter
on r-anndata
on r-base
>=4.4,<4.5.0a0on r-coloc
on r-data.table
on r-dplyr
on r-matrix
on r-optparse
on r-susier
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install r-flanders
to add into an existing workspace instead, run:
pixi add r-flanders
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install r-flanders
Alternatively, to install into a new environment, run:
conda create -n envname r-flanders
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/r-flanders:<tag>
(see r-flanders/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/r-flanders/README.html)
