NetCIS: Network-based Common Insertion Site analysis

BridGE: a pathway-based analysis tool for detecting genetic interactions from GWAS

A fast, precise, pure Python implementation of Fisher's exact test

upload big files to Zenodo using cURL, jq and bash

Application for making ENCODE Blacklists

A curated list of awesome places to learn and/or practice algorithms.

Codebase for information theoretic shapley values to explain predictive uncertainty.This repo contains the code related to the paperWatson, D., O'Hara, J., Tax, N., Mudd, R., & Guy, I. (2023). Expl…

AlphaFold 3 inference pipeline.

Pangenome-based genome inference

the pangenome graph builder

A comprehensive guide to applying statistical techniques in machine learning, including data preprocessing, model development, evaluation metrics, and real-world applications. This repository provi…

MMseqs2: ultra fast and sensitive search and clustering suite

Metric Learning on L1K, and other datasets

Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)

Python library to handle Gene Ontology (GO) terms

Diffusion model for gene regulatory network inference.

Linear-time de novo Long Read Assembler

Official home of genome aligner based upon notion of Cactus graphs

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Sequence-to-graph mapper and graph generator

tools for working with genome variation graphs

Python based GBDT implementation on GPU. Efficient multioutput (multiclass/multilabel/multitask) training

A library for efficient similarity search and clustering of dense vectors.

Cython implementation of the adaptive k-nearest-neighbor algorithm

an easy-to-use knn-mt toolkit

A toolkit for single-cell immune profiling