Table Transformer (TATR) is a deep learning model for extracting tables from unstructured documents (PDFs and images). This is also the official repository for the PubTables-1M dataset and GriTS ev…

PyMuPDF is a high performance Python library for data extraction, analysis, conversion & manipulation of PDF (and other) documents.

Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

Open source implementation of AlphaFold3

Retrieve author and publication information from Google Scholar in a friendly, Pythonic way without having to worry about CAPTCHAs!

Fetch Academic Research Papers from different sources

PyPaperBot is a Python tool for downloading scientific papers using Google Scholar, Crossref, SciHub, and SciDB.

Sorting Google Scholar search results based on the number of citations

High-Resolution Epidemiological Landscape from 290K SARS-CoV-2 Genomes from Denmark

The fastai book, published as Jupyter Notebooks

Annotated data.

Minimalist LaTeX template for academic papers

A beginner's guide to setting up a development environment on macOS

The repository provides code for running inference with the Meta Segment Anything Model 2 (SAM 2), links for downloading the trained model checkpoints, and example notebooks that show how to use th…

MLX: An array framework for Apple silicon

Workflow to assign Taxonomy to a bacteriophage genome isolate

A pandoc LaTeX template to convert markdown files to PDF or LaTeX.

Write beautifully typeset academic texts with distraction-free Markdown and Pandoc.

Deep mutational scanning and machine learning uncover antimicrobial peptide features driving membrane selectivity

minimal example implementations for bioinformatics workflow managers

Gunnar's 1 Billion Row Challenge (Python)

Rapidly build AI apps in Python

Positron, a next-generation data science IDE

Accelerated BLAST compatible local sequence aligner.

Repository containing R code for analysis of EHI data

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

This repository contains my PhD thesis, undertaken at Imperial College London in years 2020-2024.

Biopython Jupyter Notebook tutorial to characterize a small genome

Template and documentation on how to structure bioinformatic componenets of projects