Democratizing AI scientists with ToolUniverse

Minimalist Async Evaluation Framework for R

A GTF-native ORF annotation tool for transcriptomes

A tool for exploring large trees in the browser

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

Assembly and binning of metagenomes

The Book of Statistical Proofs

An extremely fast Python package and project manager, written in Rust.

R bindings to libarchive, supporting a large variety of archive formats

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

Using Deep Learning to predict gene annotations

This repository contains the source code of the R package for EvoGeneX, a software to infer the mode of evolution from the gene expression data.

Machine learning glossary

MAPLE - a new approximate approach for maximum likelihood phylogenetics at short divergence.

Visualize and annotate genomic coverage with ggplot2

Foundation Models for Genomics & Transcriptomics

🧬 gget enables efficient querying of genomic reference databases

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

ggplot2 extension inspired by GraphPad Prism

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

LucaVirus: Modeling the Evolutionary and Functional Landscape of Viruses with a Unified Genome-Protein Language Model

The resources of LucaOne, including: the model code, training scripts, embedding inference code, and trained checkpoints.

Mamba SSM architecture

The R Installation Manager

Code for running RFdiffusion

Bayesian Evolutionary Analysis Sampling Trees

Python for Data Science Summer Camp at College of Ecology@LZU