❄️ My nix config and dotfiles

A new high-resolution long-read metagenome assembler for even noisy reads

Genome modeling and design across all domains of life

🍁 Generate infrastructure and network diagrams directly from your NixOS configurations

Massively parallel phylogenetic placement of genetic sequences

Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes

RNA-seq prediction with deep convolutional neural networks.

Official repository for the paper "Learning from pre-pandemic data to forecast viral antibody escape"

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.

Language modeling of viral evolution

AlphaFold 3 inference pipeline.

Biological foundation modeling from molecular to genome scale

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes

Open source code for AlphaFold 2.

A list of deep learning implementations in biology

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hie…

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Tensors and Dynamic neural networks in Python with strong GPU acceleration

An Open Source Machine Learning Framework for Everyone

Jupyter notebooks for the code samples of the book "Deep Learning with Python"

Applied Computational Genomics Course at UU: Spring 2020

NGLess: NGS with less work

More scalable dereplication for metagenome assembled genomes

Phylogenetic placement and downstream analysis

ATLAS - Three commands to start analyzing your metagenome data

An analysis and visualization platform for 'omics data

Animation engine for explanatory math videos