human-cell-atlas
There are 53 repositories under human-cell-atlas topic.
satijalab/seurat
R toolkit for single cell genomics
scverse/scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
theislab/scarches
Reference mapping for single-cell genomics
spacetx/starfish
starfish: unified pipelines for image-based transcriptomics
iSEE/iSEE
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
hemberg-lab/SC3
A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
stemangiola/CuratedAtlasQueryR
Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
LuyiTian/sc_mixology
This contains the dataset for comparing scRNA-seq analysis methods
hemberg-lab/scmap
A tool for unsupervised projection of single cell RNA-seq data
theislab/cpa
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.
drisso/SingleCellExperiment
Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.
FertigLab/CoGAPS
Bayesian MCMC matrix factorization algorithm
broadinstitute/single_cell_portal_core
Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
MarioniLab/DropletUtils
Clone of the Bioconductor repository for the DropletUtils package.
broadinstitute/single_cell_portal
Tutorials, workflows, and convenience scripts for Single Cell Portal
MarioniLab/scran
Clone of the Bioconductor repository for the scran package.
Teichlab/Genes2Genes
Aligning gene expression trajectories of single-cell reference and query systems
quon-titative-biology/scAlign
A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches
morris-lab/BiddyetalWorkflow
This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.
showteeth/scfetch
Access and Format Single-cell RNA-seq Datasets from Public Resources
hemberg-lab/D3E
Discrete Distributional Differential Expression
morris-lab/CellTagR
This repository contains the CellTag data analysis R package to support clone calling and lineage reconstruction.
MarioniLab/EmptyDrops2017
Code for the empty droplet and cell detection project from the HCA Hackathon.
lasersonlab/ndarray.scala
N-dimensional arrays, with Zarr and HDF5 integrations
LTLA/batchelor
Clone of the Bioconductor repository for the batchelor package.
lasersonlab/single-cell-experiments
Experiments to run single cell analyses efficiently at scale using Zarr, anndata, Scanpy, and Apache Spark
drisso/mbkmeans
K-means clustering for large single-cell datasets
lasersonlab/zappy
Distributed processing with NumPy and Zarr
Bioconductor/HCABrowser
Browse the Human Cell Atlas data portal
federicomarini/HCAData
Access data from the Human Cell Atlas project, directly via R/Bioconductor
LTLA/MoeDCPLogo
Making the DCP logo moe-r.
satijalab/seurat-docker
Docker images of Seurat
LTLA/BiocSingular
Clone of the Bioconductor repository for the BiocSingular package.
chanzuckerberg/ontology-ui
Ontology visualizer
morris-lab/PreviousCloneHunter
This repository contains our CellTag CloneHunter R package for clone-calling.