kelly1210

AALI

Python script for checking the interactions between amino acids and ligands

ABChemoinformatics

:ab: ABC of chemoinformatics

AD_finemap

Code supporting analyses in paper on fine-mapping AD loci

af2_conformations

A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2

Algorithm

Some classic algorithmic topics

AmpUMI

Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)

autodock-vina

Protein-ligand docking code autodock vina from vina.scripps.edu

autokeras

Accessible AutoML for deep learning.

awesome-cancer-variant-databases

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

kelly1210/AD_finemap

Code supporting analyses in paper on fine-mapping AD loci

kelly1210/af2_conformations

A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2

kelly1210/CancerVar

Clinical interpretation of somatic mutations in cancer

kelly1210/clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data

kelly1210/DeepPocket

Ligand Binding Site detection using Deep Learning

kelly1210/DENTIST

DENTIST (Detecting Errors iN analyses of summary staTISTics) is a QC tool for summary-data-based analyses.

kelly1210/depmap

Cancer Dependency Map package

kelly1210/efo

Github repo for the Experimental Factor Ontology (EFO)

kelly1210/EMOGI

An explainable multi-omics graph integration method based on graph convolutional networks to predict cancer genes.

kelly1210/genetics-sumstat-harmoniser

Harmonise GWAS summary statistics against a reference VCF

kelly1210/HiTEA

The High Throughput Experimentation Analyzer (HiTEA) modules as described in "Probing the Chemical 'Reactome' with High Throughput Experimentation Data" (King-Smith et al.).

kelly1210/MassSpecBlocks

MassSpecBlocks is open source, web application to manage own user databases of chemical structures like NRPs and to find structures on other chemical projects.

kelly1210/MD-IFP

MD trajectory analysis using protein-ligand Interaction Fingerprints

kelly1210/MODIFY

ML-optimized library design with improved fitness and diversity for protein engineering

kelly1210/openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

kelly1210/openpbs

An HPC workload manager and job scheduler for desktops, clusters, and clouds.

kelly1210/PBDEL

kelly1210/PRosettaC

kelly1210/ProtLGN

kelly1210/PyAutoFEP

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods

kelly1210/pyfoldx

pyFoldX: python bindings for FoldX.

kelly1210/PyPDF2

A utility to read and write PDFs with Python

kelly1210/ReSimNet

Implementation of ReSimNet for drug response similarity prediction

kelly1210/RoseTTAFold

This package contains deep learning models and related scripts for RoseTTAFold

kelly1210/RoseTTAFold-All-Atom

kelly1210/RoseTTAFold2NA

RoseTTAFold2 protein/nucleic acid complex prediction

kelly1210/skywalkR

code for Gogleva et al manuscript

kelly1210/skywalkR-graph-features

Example notebooks that illustrate how to generate knowledge-based features. Features can be used in a variety of ML models, including recommender systems.

kelly1210/Synt-On

Open-source tool for synthons-based library design.

kelly1210/tractability_pipeline_v2

Pipeline for assessing the tractability of potential targets (starting from Gene IDs)