- recipe bioconductor-past
Pathway Association Study Tool (PAST)
GPL (>=3) + file LICENSE
PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating enrichment score and significance of pathways, and plotting pathways.
- package bioconductor-past¶
- depends bioconductor-genomicranges:
- depends bioconductor-qvalue:
- depends bioconductor-rtracklayer:
- depends bioconductor-s4vectors:
- depends r-base:
- depends r-doparallel:
- depends r-dplyr:
- depends r-foreach:
- depends r-ggplot2:
- depends r-iterators:
- depends r-rlang:
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-past and update with:: mamba update bioconductor-past
To create a new environment, run:
mamba create --name myenvname bioconductor-past
myenvnamebeing 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/bioconductor-past:<tag> (see `bioconductor-past/tags`_ for valid values for ``<tag>``)