zachcp

ReLaXed

Create PDF documents using web technologies

pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

linter-rules-for-nextflow

Linter rules for Nextflow DSL scripts

egapx

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

DiffDock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

storm

An LLM-powered knowledge curation system that researches a topic and generates a full-length report with citations.

xq

Command-line XML and HTML beautifier and content extractor

xh

Friendly and fast tool for sending HTTP requests

BiologicalTokenizers

Effect of tokenization on transformers for biological sequence

mxfold2

MXfold2: RNA secondary structure prediction using deep learning with thermodynamic integration

ms2rescore-rs

Rust functionality for the MS²Rescore package

megablocks

feature-viewer

Library to visualize protein sequence features in javascript using D3 - From SIB CALIPHO group; neXtProt project

orthanq

Haplotype quantification - HLA type prediction and viral lineage quantification from NGS data

rust-superkmers

Construction of superkmers from a DNA sequence in rust

icons

All SVG icons available on https://game-icons.net

heme_binder_diffusion

NextPolish2

Repeat-aware polishing genomes assembled using HiFi long reads

logos

Create ridiculously fast Lexers

protein_bert

ProteinNPT

Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"

enz-pred

enzyme-datasets

Enzyme datasets used to benchmark enzyme-substrate promiscuity models

ASKCOS

Software package for computer aided synthesis planning

rdchiral

Wrapper for RDKit's RunReactants to improve stereochemistry handling

bkms-data

retrosim_enz

Enzymatic retrosynthesis by similarity

sequence_align

Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.

palmscan

Triton-Puzzles

Puzzles for learning Triton