enrichrpy 0.1.0

A tool for gene set enrichment (GSEA) plots and analysis in Python. Built on top of Enrichr API.

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.

Note, all plots generated by enrichrpy are created by altair, so they can be easily downloaded as either .svg or .png files from your browser.

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

Enrichment bar plot

epl.enrichment_barplot(df, n=20)

Enrichment dot plot

epl.enrichment_dotplot(df, n=20, hue='Z-score', log=True)