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human-cell-atlas

Here are 53 public repositories matching this topic...

satijalab / seurat

R toolkit for single cell genomics

cran single-cell-genomics single-cell-rna-seq human-cell-atlas

Updated Apr 10, 2024
R

scverse / scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

deep-learning scrna-seq variational-autoencoder variational-bayes single-cell-genomics single-cell-rna-seq deep-generative-model cite-seq human-cell-atlas scverse

Updated Apr 24, 2024
Python

theislab / scarches

Reference mapping for single-cell genomics

deep-learning scrna-seq data-integration single-cell rna-seq-analysis single-cell-genomics batch-correction multimodal-deep-learning multiomics human-cell-atlas

Updated Apr 9, 2024
Jupyter Notebook

spacetx / starfish

starfish: unified pipelines for image-based transcriptomics

python transcriptomics imaging human-cell-atlas

Updated Mar 21, 2024
Python

iSEE / iSEE

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

visualization gui shiny clustering gene-expression feature-extraction transcriptomics single-cell hacktoberfest dimension-reduction human-cell-atlas

Updated Apr 4, 2024
R

hemberg-lab / SC3

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

single-cell-rna-seq bioconductor-package human-cell-atlas

Updated Jun 28, 2021
R

LuyiTian / sc_mixology

This contains the dataset for comparing scRNA-seq analysis methods

benchmarking dataset human-cell-atlas

Updated Aug 26, 2020
HTML

hemberg-lab / scmap

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

r projection-mapping single-cell-rna-seq bioconductor-package human-cell-atlas

Updated Nov 24, 2020
R

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.

scrna-seq single-cell-genomics single-cell-rna-seq human-cell-atlas

Updated Mar 31, 2024
Python

stemangiola / CuratedAtlasQueryR

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

database tidyverse hdf5 single-cell human-cell-atlas singlecellexperiment duckdb

Updated Apr 26, 2024
R

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.

bioconductor single-cell-rna-seq bioconductor-package human-cell-atlas

Updated Mar 27, 2024
R

broadinstitute / single_cell_portal_core

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

rna-seq-analysis single-cell-genomics human-cell-atlas

Updated Apr 26, 2024
Ruby

MarioniLab / DropletUtils

Clone of the Bioconductor repository for the DropletUtils package.

single-cell-rna-seq bioconductor-package human-cell-atlas

Updated Mar 12, 2024
R

CoGAPS

FertigLab / CoGAPS

Bayesian MCMC matrix factorization algorithm

machine-learning bioinformatics bayesian-inference single-cell-rna-seq non-negative-matrix-factorization human-cell-atlas

Updated Apr 9, 2024
C++

broadinstitute / single_cell_portal

Tutorials, workflows, and convenience scripts for Single Cell Portal

rna-seq-analysis single-cell-genomics human-cell-atlas

Updated Mar 5, 2024
HTML

MarioniLab / scran

Clone of the Bioconductor repository for the scran package.

single-cell-rna-seq bioconductor-package human-cell-atlas

Updated Mar 2, 2024
R

quon-titative-biology / scAlign

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

scrna-seq single-cell single-cell-genomics scrna-seq-analysis human-cell-atlas

Updated Nov 16, 2021
R

tallulandrews / M3Drop

rna-seq single-cell single-cell-rna-seq human-cell-atlas

Updated Mar 4, 2024
R

morris-lab / BiddyetalWorkflow

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

human-cell-atlas

Updated Aug 29, 2019
R

showteeth / scfetch

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

geo bam fastq zenodo sra single-cell-rna-seq format-conversion-tool human-cell-atlas cellxgene panglaodb ucsc-cell-browser

Updated Dec 30, 2023
R

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