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33 search results found

Seurat ⭐ 2,025

R toolkit for single cell genomics

Scvi Tools ⭐ 1,140

Deep probabilistic analysis of single-cell and spatial omics data

Scarches ⭐ 294

Reference mapping for single-cell genomics

Starfish ⭐ 220

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

Awesome Expression Browser ⭐ 107

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

Curatedatlasqueryr ⭐ 70

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

Sc_mixology ⭐ 69

This contains the dataset for comparing scRNA-seq analysis methods

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

Single_cell_portal_core ⭐ 60

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

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

Singlecellexperiment ⭐ 52

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

Single_cell_portal ⭐ 41

Tutorials, workflows, and convenience scripts for Single Cell Portal

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

Biddyetalworkflow ⭐ 27

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

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

Emptydrops2017 ⭐ 13

Code for the empty droplet and cell detection project from the HCA Hackathon.

Discrete Distributional Differential Expression

Celltagr ⭐ 13

This repository contains the CellTag data analysis R package to support clone calling and lineage reconstruction.

Ontoprocpre2021 ⭐ 9

Ontology processing for Bioconductor

Ndarray.scala ⭐ 9

N-dimensional arrays, with Zarr and HDF5 integrations

Hcabrowser ⭐ 8

Browse the Human Cell Atlas data portal

K-means clustering for large single-cell datasets

Single Cell Experiments ⭐ 7

Experiments to run single cell analyses efficiently at scale using Zarr, anndata, Scanpy, and Apache Spark

Moedcplogo ⭐ 7

Making the DCP logo moe-r.

Access data from the Human Cell Atlas project, directly via R/Bioconductor

Previousclonehunter ⭐ 6

This repository contains our CellTag CloneHunter R package for clone-calling.

Distributed processing with NumPy and Zarr

Query Service ⭐ 5

Prototype implementation of the DCP Query Service, a metadata search engine for HCA

Ontology Ui ⭐ 5

Ontology visualizer

Related Searches

R Human Cell Atlas (16)

Python Human Cell Atlas (8)

1-33 of 33 search results

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