R toolkit for single cell genomics
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Updated
May 8, 2024 - R
R toolkit for single cell genomics
Deep probabilistic analysis of single-cell and spatial omics data
Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
Access and Format Single-cell RNA-seq Datasets from Public Resources
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
Access data from the Human Cell Atlas project, directly via R/Bioconductor
Bayesian MCMC matrix factorization algorithm
Aligning gene expression trajectories of single-cell reference and query systems
Reference mapping for single-cell genomics
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.
Clone of the Bioconductor repository for the beachmat package.
Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.
Download fastqs or supplementary files from GEO and upload to hca-util bucket
starfish: unified pipelines for image-based transcriptomics
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.
Add a description, image, and links to the human-cell-atlas topic page so that developers can more easily learn about it.
To associate your repository with the human-cell-atlas topic, visit your repo's landing page and select "manage topics."