Proteogenomics database-generation tool for protein haplotypes and variants

MaveDB API

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.

Genomic sequence preprocessing toolkit

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

RNA-seq prediction with deep convolutional neural networks.

Dataloader for applying sequence models to personalized genomics

Code for embedding human phenotype ontology (HPO) using Node2Vec and incorporating phenotype frequencies from a hospital-size dataset. Showcased in the linked paper.

mOWL: Machine Learning library with Ontologies

The official SNOMED CT OWL Toolkit. OWL conversion, classification and authoring support.

Scaling Single Cell Analysis to Millions of Cells

Genotype Representation Graph Library

Functional Embedding of Gene Signatures

This repository contains the python package for Helical

CZ CELLxGENE Discover Census

A package for ontology engineering with deep learning and language models.

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

Access Amazon Web Service 'S3' as if it were a file system. File system 'API' design around R package 'fs'

My CV built using RMarkdown and the pagedown package.

R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)

Semantic prefix map registry

Dimension Reduction and Estimation Methods

Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks

An R package to query EBI's Ontology Lookup Service (OLS)

GWAS Summary Statistics Data Harmonisation

Bioconductor working group guidelines. Also, a list of active, suggested, and inactive working groups for bioconductor for the community to volunteer to be apart of. The community is also welcome t…

scOntoMatch is an R package which unifies ontology annotation of scRNA-seq datasets to make them comparable across studies

gwasrapidd: an R package to query, download and wrangle GWAS Catalog data