UC, San Diego Trey Ideker Lab

Bioinformatics software projects developed by UCSD Trey Ideker lab

La Jolla, CA USA

Pinned Repositories

cy-rest-R
Example R script to use Cytoscape via RESTful API module.
Language:HTML27 19 313
cyREST
DEPRECATED. Please visit our new repository (cytoscape/cyREST)
Language:Java28 14 4114
DCell
DCell browser and gene deletion simulator
Language:JavaScript117 19 3834
DrugCell
A visible neural network model for drug response prediction
Language:Python121 11 2554
hiview
HiView: the universal viewer for hierarchical data
Language:JavaScript16 6 377
MuSIC
Multi-Scale Integrated Cell
Language:Python35 11 18
Network_Evaluation_Tools
Python 2.7 package with examples for evaluating a network's ability to group a given node set in network proximity.
Language:Jupyter Notebook32 8 219
pyNBS
Python 2.7 implementation of network-based stratification (NBS) algorithm from Hofree et al (Nature Methods 2013)
Language:Jupyter Notebook37 6 622
TCRP
Few shot learning for cancer
Language:Python34 8 110
vizbi-2015
Sample data and notebooks for VIZBI 2015 tutorial session
5 7 112

UC, San Diego Trey Ideker Lab's Repositories

idekerlab/DrugCell
A visible neural network model for drug response prediction
Language:Python121 11 2554
idekerlab/KEGGscape
A Cytoscape app for importing KGML(KEGG pathway XML)
Language:Java21 13 2410
idekerlab/heat-diffusion
Language:Python12 8 19
idekerlab/llm_evaluation_for_gene_set_interpretation
Code space for 'Evaluation of large language models for discovery of gene set function'
Language:Jupyter Notebook10 8 23
idekerlab/cy-net-share
A simple web application to share network files generated with Cytoscape.
Language:JavaScript9 7 167
idekerlab/nest_vnn
NeST-VNN repo
Language:Python9 9 33
idekerlab/web.cytoscape
New version of cyNetShare
Language:JavaScript7 6 11
idekerlab/cellmaps_pipeline
Language:Python4 5 3
idekerlab/auto-graph-visualizer
Automatic graph visualizer for the Cytoscape ecosystem
Language:Python3 7 31
idekerlab/large-graph-renderer
Webpack version of LGR
Language:TypeScript21
idekerlab/multitask_vnn
Multi-task learning VNN
Language:Python2 6 02
idekerlab/cdhidef
Language:Python1 6 1
idekerlab/cellmaps_annotate_hierarchy
Language:Jupyter Notebook1 7 00
idekerlab/cellmaps_utils
Language:Python1 6 2
idekerlab/GSAI
Language:TypeScript1
idekerlab/network-viewer
Language:TypeScript1 4 0
idekerlab/qfieldlayout
Language:Python1 7 0
idekerlab/cellmaps_coembedding
Language:Python0 5 20
idekerlab/cellmaps_hierarchyeval
Code for hierarchy evaluation
Language:Python0 3 20
idekerlab/cdapsutil
Language:Python2 1
idekerlab/cdiquerygenestoterm
Language:Python5 0
idekerlab/cellmaps_generate_hierarchy
Language:Python5 6
idekerlab/cellmaps_image_embedding
Language:Python5 3
idekerlab/cellmaps_imagedownloader
Language:Python5 7
idekerlab/cellmaps_ppi_embedding
Language:Python5 21
idekerlab/cellmaps_ppidownloader
Language:Python5 4
idekerlab/cellmaps_vnn
Language:Python6 2
idekerlab/cookiecutter-musicpypackage
Language:Python5 0
idekerlab/hicomp
Language:Python5 0
idekerlab/ndex-edge-filter4Hiview
An edge filtering service for Hiview.
Language:Java3 0