Quickstart Guide

Get started with DILImap in just a few steps.

Install DILImap using:

pip install dilimap

DILImap workflow

Import the package:

import dilimap as dmap

Read your dataset (.h5ad or .csv format):

adata = dmap.read(filename)

Don’t have a dataset yet? Use a built-in demo:

adata = dmap.datasets.demo_data()

Apply quality control to filter out low-quality samples:

dmap.pp.qc_metrics(adata, **params)
dmap.pp.qc_cross_rep_correlation(adata, **params)

Run DESeq2 to compute differential gene expression:

adata_deseq = dmap.pp.deseq2(adata, **params)

Compute pathway-level signatures from DESeq2 results:

FDR = adata_deseq.to_df('FDR')
adata_wp = dmap.pp.pathway_signature(FDR, **params)

Apply the DILI prediction model:

model = dmap.models.ToxPredictor('v1')
df_results = model.predict(adata_wp, **params)

Estimate safety margins:

df_margins = model.compute_safety_margins(adata_wp, **params)

Generate dose-response plots per compound:

model.plot_DILI_dose_regimes(cmpd, **params)