gonzalobenegas

faiss

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

al-folio

A beautiful, simple, clean, and responsive Jekyll theme for academics

miller

Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON

pandarallel

A simple and efficient tool to parallelize Pandas operations on all available CPUs

copilot.el

An unofficial Copilot plugin for Emacs.

zarr-python

An implementation of chunked, compressed, N-dimensional arrays for Python.

curated-transformers

🤖 A PyTorch library of curated Transformer models and their composable components

MEGABYTE-pytorch

Implementation of MEGABYTE, Predicting Million-byte Sequences with Multiscale Transformers, in Pytorch

cactus

Official home of genome aligner based upon notion of Cactus graphs

pyranges

Performant Pythonic GenomicRanges

basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

datasets

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

scidataflow

Command line scientific data management tool

ProteinGym

Official repository for the ProteinGym benchmarks

gpn

Genomic Pre-trained Network

WiggleTools

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency

tangermeme

Biological sequence analysis for the modern age.

granges

A Rust library and command line tool for working with genomic ranges and their data.

BEND

Benchmarking DNA Language Models on Biologically Meaningful Tasks

borzoi

RNA-seq prediction with deep convolutional neural networks.

MARVEL

taffy

This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files

MAGE

Analysis of gene expression and splicing diversity in a subset of samples from the 1000 Genomes Project, including eQTL and sQTL discovery and annotation.

poranges

pyranges/bioframe for polars

ldgm

Software for linkage disequilibrium graphical models

scquint

Conservatory

Identification of conserved non-coding sequences in plants

LLM_eval

Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"

HOTFOXES

Scripts for Rocha et al. 2023: "North-African fox genomes show signatures of repeated introgression and adaptation to life in deserts"

scquint-analysis