idekerlab/llm_evaluation_for_gene_set_interpretation

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Created about 1 year ago
Updated 4 months ago

idekerlab/llm_evaluation_for_gene_set_interpretation

idekerlab

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Code space for 'Evaluation of large language models for discovery of gene set function'

DrugCell

A visible neural network model for drug response prediction

DCell

DCell browser and gene deletion simulator

pyNBS

Python 2.7 implementation of network-based stratification (NBS) algorithm from Hofree et al (Nature Methods 2013)

Jupyter Notebook

MuSIC

Multi-Scale Integrated Cell

TCRP

Few shot learning for cancer

Network_Evaluation_Tools

Python 2.7 package with examples for evaluating a network's ability to group a given node set in network proximity.

Jupyter Notebook

cyREST

DEPRECATED. Please visit our new repository (cytoscape/cyREST)

cy-rest-R

Example R script to use Cytoscape via RESTful API module.

hiview

HiView: the universal viewer for hierarchical data

heat-diffusion

cy-rest-python

cyREST examples for Python users.

cy-net-share

A simple web application to share network files generated with Cytoscape.

nexo

Prototype for NeXO web app.

tsri-lecture

Course material for TSRI network biology lecture

Jupyter Notebook

dot-app

Cytoscape application for exporting to .dot file format

web.cytoscape

New version of cyNetShare

vizbi-2015

Sample data and notebooks for VIZBI 2015 tutorial session

jActiveModules

cellmaps_pipeline

cy-rest-node

Node.js examples for cyREST module.

cxmateold

A RESTFUL network API proxy service for network algorithms

sdcsb-advanced-tutorial

Course material for SDCSB Advanced Cytoscape Workshop (4/17/2015)

auto-graph-visualizer

Automatic graph visualizer for the Cytoscape ecosystem

neoelsa

ce-components

Example implementation for CE component collection

large-graph-renderer

Webpack version of LGR

multitask_vnn

Multi-task learning VNN

BiNGO

ci-service-template

Template code to create new Cytoscape CI services.

TreeViewer

D3-based DAG viewer for DCell web applicaiton

cyrest-examples

Latest example notebooks for CyREST

Jupyter Notebook

nest_vnn

VNN for drug response using NeST

qfieldlayout

obo-exporter

Jupyter Notebook

cellmaps_annotate_hierarchy

Jupyter Notebook

network-viewer

cdhidef

webservice-ncbi-client

NCBI Client for CYtoscape 3. Moved from the core.

ndex-web

React webapp code for CyNDEx2 Cytoscape App

diffusion-old

Heat diffusion daemon

Automatic_graph_visualizer

Jupyter Notebook

cy-components

Monorepo for all React components maintained by Ideker Lab

drugcell-web-app

nexo-client

Client side module for NeXO web app.

cdoslom

Packaged OSLOM algorithm towards standardized community detection services for Cytoscape

cellmaps_utils

cxio_python

ddot_rest_server

NBGWAS-Frontend

A ReactJS Frontend page for the NBGWAS service created by Samson Fong and Dan Carlin

science-direct-app

cyEZVis

Adding support for CalVR via Mugic plugin.

ndex-valet-electron

NDEx Valet Electron app

GSAI