Pinned Repositories
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.
CellAnnotationTutorial
Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
Cytoscape_workflows
collection of notebooks with different cytoscape workflows
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 populations
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.
scClustViz
Explore and share your scRNAseq clustering results
Tempora
Pathway-based trajectory inference method for time-series scRNAseq data
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.
Bader Lab, University of Toronto's Repositories
BaderLab/CellAnnotationTutorial
Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
BaderLab/Cytoscape_workflows
collection of notebooks with different cytoscape workflows
BaderLab/scClustViz
Explore and share your scRNAseq clustering results
BaderLab/EnrichmentMapApp
The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
BaderLab/ecuda
STL-like containers (array, vector, matrix, cube) useable in device code.
BaderLab/netDx
R package with netDx software and data for examples
BaderLab/MALAT1_threshold
BaderLab/CCInx
Build predicted cell-cell interaction networks from single-cell data.
BaderLab/AutoAnnotateApp
The AutoAnnotate Cytoscape App finds clusters of nodes and visually annotates them with semantic labels and groups.
BaderLab/MCODE
Cytoscape app that clusters a given network based on topology to find densely connected regions
BaderLab/openPIP
The open protein interaction platform repo
BaderLab/SocialNetworkApp
dropbox
BaderLab/GeneEval
A Python library for evaluating gene embeddings.
BaderLab/EnrichmentMap_docs
End-User Documentation for the EnrichmentMap Cytoscape App
BaderLab/EnrichmentMap_monthlyGenesetBuild
BaderLab/CBW_Pathways_2023
CBW Pathway and Network Analysis Bookdown for June 2023
BaderLab/RatLiver
a single-cell atlas of the rat liver
BaderLab/RETINA
BaderLab/ALS_APA
Codes for APA-Net model and analysis for ALS APA atlas paper
BaderLab/APA-Net
BaderLab/HealthyRatLiverMap
BaderLab/Baderlab_static_webservers
repo with dockers for each of the static baderlab servers
BaderLab/CBW_Pathways_2024
CBW Pathway and Network Analysis Bookdown for June 2024
BaderLab/CBW_Pathways_2024_asynchronous
CBW Asynchronous Pathway and Network Analysis Bookdown for November 2024
BaderLab/Chan-Covid19
Code for Chan lab collaboration for Covid-19 research
BaderLab/DoMo-Pred-Human
Predicting SH3 domain mediated protein interactions in human
BaderLab/FLASH-MM
Fast and scalable LMM estimation algorithm for differential expression (DE) analysis of scRNA-seq
BaderLab/FLASHMM
Fast and Scalable Single Cell Differential Expression Analysis using Mixed-effects Models
BaderLab/logrank.test_power
R function and document for power analysis of the log-rank test in survival analysis
BaderLab/mimp_webserver
code to run the mimp webserver (mimp.baderlab.org)