Discover BaderLab/AutoAnnotateApp Open Source project

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

102

CellAnnotationTutorial

HTML

Cytoscape_workflows

collection of notebooks with different cytoscape workflows

HTML

scClustViz

Explore and share your scRNAseq clustering results

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.

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.

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

ecuda

C++

EnrichmentMapApp

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

R Data: Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

HumanLiver

Tempora

Pathway-based trajectory inference method for time-series scRNAseq data

singleLiverCells

Scripts for processing single liver cells RNA-Seq 10X Genomics Data

AgingMouseBrainCCInx

Predicted cell-cell interactions of the aging mouse brain

EPIC

This is the public repository for the EPIC tool.

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".

Towards-reliable-BioNER

R package with netDx software and data for examples

netDx

scRNAseqWorkflow

Brendan's skeleton scRNAseq workflow using scran, Seurat, and scClustViz

MALAT1_threshold

GenomeClinic-PGX

Web application for clinical pharmacogenomic interpretation

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

CCInx

HTML

cy3d-impl

3D Graph Renderer for Cytoscape using OpenGL

The open protein interaction platform repo

openPIP

Cytoscape app that clusters a given network based on topology to find densely connected regions

MCODE

SocialNetworkApp

dropbox

A Python library for evaluating gene embeddings.

GeneEval

R data: Developmental emergence of adult neural stem cells as revealed by single cell transcriptional profiling

MouseCortex

EM-tutorials-docker

Jupyter Notebook

EnrichmentMap_docs

End-User Documentation for the EnrichmentMap Cytoscape App

Cell_Cycle_Theory

Mathematica

EnrichmentMap_monthlyGenesetBuild

Suite of wrappers for CyREST functions in R

EasycyRest

WordCloudPlugin

WordCloud Cytoscape app

Pharmacogenomics app for MedSavant

Cytoscape-workshop-docker

Jupyter Notebook

pharmacogenomics

A BioPAX to/from JSON-LD format converter.

biopax-jsonld

Web Ontology Language

covid19-dashboard

Population-based pathway analysis of SNP-SNP coevolution

POPPATHR

StudentProjectIdeas

Project ideas for summer and co-op students

PNC_PathwayAnalysis

Pathway analysis pipeline for PNC data (GWAS + GSEA)

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

BreastCancer_PathwayAnalysis

a single-cell atlas of the rat liver

RatLiver

SummExpDR

Wrapper for SummarizedExperiment Objects for performing data integration + dimensionality reduction

gproxy

A proxy server for Google Analytics to bypass adblockers etc

Introductory workshop for cytoscape automation with RCy3

Rcy3IntroWorkshop

PromoterPredictor

Using a SVM and 5 identified features, scan genomic coordinates for putative promoter regions