A tutorial on how to annotate and interpret novel mammalian reference genomes

Fast and Scalable Single Cell Differential Expression Analysis using Mixed-effects Models

Graph theory (network) library for visualisation and analysis

Wrapper for SummarizedExperiment Objects for performing data integration + dimensionality reduction

Cytoscape.js plugin for simplified layers (svg, canvas, html)

Overview of the P4GDA material

PathwayCommons v12 on Virtuoso 7

EnrichmentMap.org

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

A Node.js package that renders images of Cytoscape.js graphs on the server using Puppeteer

Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data

This is the public repository for the EPIC tool.

Network visualization webapp.

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

Biological Network Integration using Convolutions

R toolkit for single cell genomics

Cytoscape: an open source platform for network analysis and visualization

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

R package with netDx software and data for examples

Explore and share your scRNAseq clustering results

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…

easy access to benchmark datasets

View biological networks via Cytoscape.js and sbgn-ml

Cytoscape 3 implementation bundles.