bioconda / packages / bioconductor-npgsea 1.30.0

Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)

Installers

Info: This package contains files in non-standard labels.

conda install

  • linux-64  v1.16.0
  • osx-64  v1.14.0
  • noarch  v1.30.0
To install this package with conda run one of the following:
conda install -c bioconda bioconductor-npgsea
conda install -c bioconda/label/gcc7 bioconductor-npgsea
conda install -c bioconda/label/cf201901 bioconductor-npgsea

Description

Current gene set enrichment methods rely upon permutations for inference. These approaches are computationally expensive and have minimum achievable p-values based on the number of permutations, not on the actual observed statistics. We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics. We are able to reduce the computational burden and granularity issues of permutation testing with our method, which is implemented in this package. npGSEA calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results.


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