bioinformatics tools running on modal

Multi-Omics Peptide Generator

Techniques and numbers for estimating system's performance from first-principles

Self/non-self discrimination as a statistical problem

A toolkit for building Python extensions in Zig.

Effortless argument parser

20+ high-performance LLMs with recipes to pretrain, finetune and deploy at scale.

STAPLER (Shared TCR And Peptide Language bidirectional Encoder Representations from transformers) is a language model that uses a joint TCRab-peptide input to predict TCRab-peptide specificity.

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Open source code for AlphaFold 2.

Open Targets evidence normalization and scoring pipeline

The Journal of Open Source Software

Code for the paper "Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer"

This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

Structural variant and indel caller for mapped sequencing data

command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwig

ERGO is a deep learing based model for predicting TCR-peptide binding.

Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Reference-free variant discovery in large eukaryotic genomes

Quickly search, compare, and analyze genomic and metagenomic data sets.

don't get DUP'ed or DEL'ed by your putative SVs.

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection