- recipe bioconductor-gigsea
Genotype Imputed Gene Set Enrichment Analysis
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/GIGSEA.html
- License:
LGPL-3
- Recipe:
We presented the Genotype-imputed Gene Set Enrichment Analysis (GIGSEA), a novel method that uses GWAS-and-eQTL-imputed trait-associated differential gene expression to interrogate gene set enrichment for the trait-associated SNPs. By incorporating eQTL from large gene expression studies, e.g. GTEx, GIGSEA appropriately addresses such challenges for SNP enrichment as gene size, gene boundary, SNP distal regulation, and multiple-marker regulation. The weighted linear regression model, taking as weights both imputation accuracy and model completeness, was used to perform the enrichment test, properly adjusting the bias due to redundancy in different gene sets. The permutation test, furthermore, is used to evaluate the significance of enrichment, whose efficiency can be largely elevated by expressing the computational intensive part in terms of large matrix operation. We have shown the appropriate type I error rates for GIGSEA (<5%), and the preliminary results also demonstrate its good performance to uncover the real signal.
- package bioconductor-gigsea¶
- Versions:
1.28.0-0,1.24.0-0,1.20.0-1,1.20.0-0,1.18.0-0,1.16.0-0,1.12.0-0,1.10.0-0,1.8.0-1,1.28.0-0,1.24.0-0,1.20.0-1,1.20.0-0,1.18.0-0,1.16.0-0,1.12.0-0,1.10.0-0,1.8.0-1,1.8.0-0,1.6.0-0,1.4.0-0,1.2.0-1,1.2.0-0,1.0.0-0- Depends:
on r-base
>=4.5,<4.6.0a0on r-locfdr
on r-mass
on r-matrix
- 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 bioconductor-gigsea
to add into an existing workspace instead, run:
pixi add bioconductor-gigsea
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 bioconductor-gigsea
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-gigsea
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/bioconductor-gigsea:<tag>
(see bioconductor-gigsea/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/bioconductor-gigsea/README.html)
