human-cell-atlas

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

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.

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

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

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

This contains the dataset for comparing scRNA-seq analysis methods

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

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

Bayesian MCMC matrix factorization algorithm

Clone of the Bioconductor repository for the DropletUtils package.

Tutorials, workflows, and convenience scripts for Single Cell Portal

Clone of the Bioconductor repository for the scran package.

GEfetch2R - Access Single-cell/Bulk RNA-seq Data from Public Repositories and Benchmark the Subsequent Format Conversion Tools

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