wang-lab-ucsd Goto Github PK

antibody_engineering_scoring

Compares simple models (xgboost, xgpr) with fine-tuned LLMs / embeddings on some antibody property prediction tasks

antpack

Tools for annotation, processing and ML for antibody sequences

benchmarking_xgpr

The code needed to reproduce the experiments associated with Parkinson et al. 2023 for the xGPR library

cbx1_protein_engineering

Machine-learning based techniques for identifying likely strong binders from high-throughput datasets

episig

findram

Identify the modular organization of 3D genome from histone modifications. For details, please check here (https://github.com/LinaZhengUCSD/findRAM.git)

generating_projections

Generating 2d projections on random planes for randomly selected pdb structures

mepigram

Methylated DNA motif discovery tool

motif_finding_contextual_regression

motto

resp

The code used to generate the results from Parkinson / Hard et al. 2022

somaticmutation

taiji

All-in-one analysis pipeline

taiji-reprogram

tip-ra-cs

The code needed to reproduce the analysis of methylation array data in James, Holers, Iyer, Prideaux, et al. 2023.

tuna

TUnA: Transformer-based Uncertainty Aware model for PPI Prediction

uncertaintyawaredeeplearn

A PyTorch class that implements an approximate Gaussian process as the last layer of a neural network