A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.

Computational analysis of RPL22 alterations and impact on MDM4 splicing

cgat-apps repository

🎨 Visualisation toolbox for beautiful and publication-ready figures

Text and code for the second edition of Think Bayes, by Allen Downey.

Tidy Plots for Scientific Papers

Survival Analysis and Visualization

updates to PEGG package

ProCyon: A multimodal foundation model for protein phenotypes

PyGWalker: Turn your pandas dataframe into an interactive UI for visual analysis

PyTorch Extension Library of Optimized Autograd Sparse Matrix Operations

KGWAS: novel genetics discovery enabled by massive functional genomics knowledge graph

NEFF Calculator and MSA File Converter

import package_root # into your PYTHONPATH

ISLP package: data and code for labs

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

Snakemake workflow for comparing E-G links to experimental data

Association analysis of genomic regions based on permutation test

XGEP for expression-based prediction of human essential genes and candidate lncRNAs in cancer cells

Analysis cell-type-specific functional gene network, with SCINET and HumanNetv3

Hetnets in Python (relocated from dhimmel/hetio)

A Finetuned model for Enhancer prediction and our generative Cumulative Enhancer Dataset

Statistical method for cell-type-specific mapping of enhancer-gene pairs with single-cell multimodal data

A curated list of Cheminformatics libraries and software.

Notebooks accompanying the paper "Navigating the pitfalls of applying machine learning in genomics"