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agingmousebrainccinx

Predicted cell-cell interactions of the aging mouse brain

als_apa

Codes for APA-Net model and analysis for ALS APA atlas paper

apa-net

autoannotateapp

The AutoAnnotate Cytoscape App finds clusters of nodes and visually annotates them with semantic labels and groups.

baderlab_static_webservers

repo with dockers for each of the static baderlab servers

biomedical-corpora

A collection of annotated biomedical corpora, which can be used for training supervised machine learning methods for various tasks in biomedical text-mining and information extraction.

biopax-jsonld

A BioPAX to/from JSON-LD format converter.

brainapp

Biologically Relevant Analysis of Interaction Networks(Brain) Cytoscape App

breastcancer_pathwayanalysis

BreastCancer Pathway Analysis performed for Nature/Nature Genetics paper 2017 (for ERNeg and Overall breast cancer)

brendan_ccinxpred

Can intercellular signals be identified by transcriptional changes?

canvd

CAN-VD - The Cancer Variants Database.

cbw_pathways_2020

CBW Pathways workshop book

cbw_pathways_2021

cbw_pathways_2023

CBW Pathway and Network Analysis Bookdown for June 2023

ccinx

Build predicted cell-cell interaction networks from single-cell data.

cell_cycle_theory

cellannotationtutorial

Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods

chan-covid19

Code for Chan lab collaboration for Covid-19 research

covid19-dashboard

cy3d-impl

3D Graph Renderer for Cytoscape using OpenGL

cytoscape-tutorials

Collection of modular Cytoscape tutorials for online presentation using reveal.js

cytoscape-workshop-docker

cytoscape_workflows

collection of notebooks with different cytoscape workflows

docker-deploy

Automatic docker deployments on git push

domo-pred-human

Predicting SH3 domain mediated protein interactions in human

easycyrest

Suite of wrappers for CyREST functions in R

ecuda

STL-like containers (array, vector, matrix, cube) useable in device code.

em-tutorials-docker

enrichmentmap_collection

Cytoscape Meta-App for the EnrichmetMap Pipline workflow.

enrichmentmapapp

The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.