racalzadilla

viscoelasticity-of-biomolecular-condensates

UniKP

CFdb-analysis

CFdb-searches

CFTK

The co-fractionation toolkit

DNABERT_2

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

DNABERT

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

HCA_Heart

This is the official repository for the Human Cell Atlas Heart project.

GeneticInheritanceGraphLibrary

geomeTRIC

Geometry optimization code that includes the TRIC coordinate system

MutationFeatures

Generate a rich feature space describing all possible mutations in a given protein sequence (+ structure)

viral_alphafold

Various Alphafold2 structures of viral proteins

Spike_structural_models_Delta_and_Omicron

Lung5loc_scRNAseq_omcr_entrygenes

ACE2 and TMPRSS2 gene expression in human lung and airways single-cell RNAseq dataset

OpenFermion

The electronic structure package for quantum computers.

TensorNetwork

A library for easy and efficient manipulation of tensor networks.

QuSpin

A python wrapper for doing ED calculations on many-body systems

SpinWaveGenie

Library for simplifying linear spin wave calculations.

pytorch-OpCounter

Count the MACs / FLOPs of your PyTorch model.

netron

Visualizer for neural network, deep learning and machine learning models

dyckkm-learning

Codebase implementing LMs for learning the Dyck-(k,m) bounded hierarchical language

torchplot

Plotting pytorch tensors made easy!

meaningful-protein-representations

mini3di

A NumPy port of the foldseek code for encoding protein structures to 3di.

comp_dnds

Measure evolutionary pressure by efficiently computing dN/dS according to the Nei-Gojobori method

phydms

phylogenetic analyses informed by deep mutational scanning data

fld

PyTorch code for FLD (Feature Likelihood Divergence), FID, KID, Precision, Recall, etc. using DINOv2, InceptionV3, CLIP, etc.

doc-ANNOVAR

Documentation for the ANNOVAR software

Fooocus

Focus on prompting and generating

self-operating-computer

A framework to enable multimodal models to operate a computer.