recipe bioconductor-intact

Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis



GPL-3 + file LICENSE



This package integrates colocalization probabilities from colocalization analysis with transcriptome-wide association study (TWAS) scan summary statistics to implicate genes that may be biologically relevant to a complex trait. The probabilistic framework implemented in this package constrains the TWAS scan z-score-based likelihood using a gene-level colocalization probability. Given gene set annotations, this package can estimate gene set enrichment using posterior probabilities from the TWAS-colocalization integration step.

package bioconductor-intact

(downloads) docker_bioconductor-intact



depends r-base:


depends r-bdsmatrix:

depends r-numderiv:

depends r-squarem:



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-intact

and update with::

   mamba update bioconductor-intact

To create a new environment, run:

mamba create --name myenvname bioconductor-intact

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<tag>

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

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