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saber
Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work in progress. Many things are broken, and the codebase is not stable.CellAnnotationTutorial
Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methodsCytoscape_workflows
collection of notebooks with different cytoscape workflowsscClustViz
Explore and share your scRNAseq clustering resultsBiomedical-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.Transfer-Learning-BNER-Bioinformatics-2018
This repository contains supplementary data, and links to the model and corpora used for the paper: Transfer learning for biomedical named entity recognition with neural networks.ecuda
STL-like containers (array, vector, matrix, cube) useable in device code.EnrichmentMapApp
The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.HumanLiver
R Data: Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populationsTempora
Pathway-based trajectory inference method for time-series scRNAseq datasingleLiverCells
Scripts for processing single liver cells RNA-Seq 10X Genomics DataEPIC
This is the public repository for the EPIC tool.Towards-reliable-BioNER
This repository contains the corpora and supplementary data, along with instructions for recreating the experiments, for our paper: "Towards reliable named entity recognition in the biomedical domain".netDx
R package with netDx software and data for examplesscRNAseqWorkflow
Brendan's skeleton scRNAseq workflow using scran, Seurat, and scClustVizMALAT1_threshold
GenomeClinic-PGX
Web application for clinical pharmacogenomic interpretationCCInx
Build predicted cell-cell interaction networks from single-cell data.cy3d-impl
3D Graph Renderer for Cytoscape using OpenGLopenPIP
The open protein interaction platform repoMCODE
Cytoscape app that clusters a given network based on topology to find densely connected regionsSocialNetworkApp
dropboxAutoAnnotateApp
The AutoAnnotate Cytoscape App finds clusters of nodes and visually annotates them with semantic labels and groups.GeneEval
A Python library for evaluating gene embeddings.MouseCortex
R data: Developmental emergence of adult neural stem cells as revealed by single cell transcriptional profilingEM-tutorials-docker
EnrichmentMap_docs
End-User Documentation for the EnrichmentMap Cytoscape AppCell_Cycle_Theory
EnrichmentMap_monthlyGenesetBuild
EasycyRest
Suite of wrappers for CyREST functions in RWordCloudPlugin
WordCloud Cytoscape appCytoscape-workshop-docker
pharmacogenomics
Pharmacogenomics app for MedSavantbiopax-jsonld
A BioPAX to/from JSON-LD format converter.covid19-dashboard
POPPATHR
Population-based pathway analysis of SNP-SNP coevolutionStudentProjectIdeas
Project ideas for summer and co-op studentsPNC_PathwayAnalysis
Pathway analysis pipeline for PNC data (GWAS + GSEA)BreastCancer_PathwayAnalysis
BreastCancer Pathway Analysis performed for Nature/Nature Genetics paper 2017 (for ERNeg and Overall breast cancer)RatLiver
a single-cell atlas of the rat liverSummExpDR
Wrapper for SummarizedExperiment Objects for performing data integration + dimensionality reductiongproxy
A proxy server for Google Analytics to bypass adblockers etcRcy3IntroWorkshop
Introductory workshop for cytoscape automation with RCy3PromoterPredictor
Using a SVM and 5 identified features, scan genomic coordinates for putative promoter regionsLove Open Source and this site? Check out how you can help us