A tool for gene set enrichment (GSEA) plots and analysis in Python. Built on top of Enrichr API.
Project description
enrichrpy
A tool for gene set enrichment (GSEA) plots and analysis in Python. Built on top of Enrichr API.
Installation
enrichrpy is easily installed with the pip package manager.
Python>=3.6 required.
pip install enrichrpy
Basic Usage
A collab notebook with basic usage examples is available here
Enrichr GSEA statistics
import enrichrpy.enrichr as een
import enrichrpy.plotting as epl
genes = [
'TYROBP', 'HLA-DRA', 'SPP1', 'LAPTM5', 'C1QB',
'FCER1G', 'GPNMB', 'FCGR3A', 'RGS1', 'HLA-DPA1',
'ITGB2', 'C1QC', 'HLA-DPB1', 'IFI30', 'SRGN',
'APOC1', 'CD68', 'HLA-DRB1', 'C1QA', 'LYZ',
'APOE', 'HLA-DQB1', 'CTSB', 'HLA-DQA1', 'CD74',
'AIF1', 'FCGR2A', 'CD14', 'S100A9', 'CTSS'
]
df = een.get_pathway_enrichment(genes, gene_set_library='GO_Biological_Process_2021')
df
[[/images/datatable.jpg|datatable]]
Enrichment bar plot
epl.enrichment_barplot(df, n=20)
[[/images/barplot.jpg|barplot]]
Enrichment dot plot
epl.enrichment_dotplot(df, n=20, hue='Z-score', log=True)
[[/images/dotplot.jpg|dotplot]]
Project details
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