Pinned Repositories
Bioinformatics-Conference-Bingo
The perfect bingo to attend a bioinformatics conference
biomedical-entity-linking
BioNEV
Code and datasets for "Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations"
ccs-prediction
Evaluating the generalizability of graph neural networks for predicting collision cross section
chemical-roles
Curation of mechanistic relations from roles in ChEBI and MeSH
clustergrammer
An interactive heatmap visualization built using D3.js
COSMOS
np-clinical-trials
Source code and data for "Natural products have increased rates of clinical trial success throughout the drug development process"
PTSDDB-Resources
Resources of the PTSD Biomarker Database
PubMed2PDF
A Python package to download full article PDFs from OA publications
ddomingof's Repositories
ddomingof/PubMed2PDF
A Python package to download full article PDFs from OA publications
ddomingof/np-clinical-trials
Source code and data for "Natural products have increased rates of clinical trial success throughout the drug development process"
ddomingof/PTSDDB-Resources
Resources of the PTSD Biomarker Database
ddomingof/rideshare-app
A web application to share rides with your work colleagues
ddomingof/biomedical-entity-linking
ddomingof/ccs-prediction
Evaluating the generalizability of graph neural networks for predicting collision cross section
ddomingof/chemical-roles
Curation of mechanistic relations from roles in ChEBI and MeSH
ddomingof/COSMOS
ddomingof/COVID-19
Supplementary code for the paper: Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19
ddomingof/covid-pathways.github.io
ddomingof/ddomingof
My Profile
ddomingof/predictme
A web application for stratification of Alzheimer's and Parkinson's disease patients
ddomingof/drug2ways
A Python package for drug discovery by analyzing causal paths on multiscale networks
ddomingof/ethnobotany
Source code and data for "Modern drug discovery using ethnobotany: A large-scale cross-cultural analysis of traditional medicine reveals common therapeutic uses"
ddomingof/famplex
Resources for grounding protein families and complexes from text and describing their hierarchical relationships.
ddomingof/GeVa_NeIF
ddomingof/gp-bench
ddomingof/indra
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
ddomingof/kgem-ensembles-in-drug-discovery
Source code and data repository for "Ensembles of knowledge graph embedding models improve predictions for drug discovery"
ddomingof/MultiGML
MultiGML
ddomingof/nodevectors
Fastest network node embeddings in the west
ddomingof/phd-commits
Functions for scraping git commits from repositories associated with a PhD (or anything else) and plotting them.
ddomingof/plant-chemical-space
Source code and data for "Exploring the known chemical space of the plant kingdom: Insights into taxonomic patterns, knowledge gaps, and bioactive regions"
ddomingof/probability_cheatsheet
A comprehensive 10-page probability cheatsheet that covers a semester's worth of introduction to probability.
ddomingof/pyobo
A programmatic interface for generating and handling OBO in Python.
ddomingof/RPath
Source code and data for "Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery"
ddomingof/simdrugs
Python notebooks for analyses and simulating drug response on patient-specific pathway signatures
ddomingof/transcriptomic-target-correlation
On the correspondence between the transcriptomic response of a compound and its targets
ddomingof/weighting-spectral-similarity
Scripts and notebooks from Weighting low-intensity MS/MS ions and m/z frequency for spectral library annotation
ddomingof/zenodo-client