R toolkit for single cell genomics

Deep probabilistic analysis of single-cell and spatial omics data

Reference mapping for single-cell genomics

starfish: unified pipelines for image-based transcriptomics

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

A tool for unsupervised projection of single cell RNA-seq data

This contains the dataset for comparing scRNA-seq analysis methods

Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

Bayesian MCMC matrix factorization algorithm

Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.

Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

Clone of the Bioconductor repository for the DropletUtils package.

Tutorials, workflows, and convenience scripts for Single Cell Portal

Aligning gene expression trajectories of single-cell reference and query systems

Clone of the Bioconductor repository for the scran package.

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

Access and Format Single-cell RNA-seq Datasets from Public Resources

This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.