scrna-seq

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

dynamo scrna-seq differential-geometry dynamical-systems vector-field scslam-seq potential-landscape nasc-seq sci-fate scnt-seq rna-velocity cell-fate rna-jacobian rna-acceleration rna-curvature rna-divergence

UpdatedFeb 20, 2026
Python

Teichlab /celltypist

Star451

A tool for semi-automatic cell type classification

python machine-learning scrna-seq single-cell cell-type-classification label-transfer

UpdatedJan 31, 2026
Python

theislab /scarches

Star398

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

UpdatedDec 2, 2025
Jupyter Notebook

junjunlab /scRNAtoolVis

Star374

Useful functions to make your scRNA-seq plot more cool!

visualization scrna-seq elegant yyds

UpdatedDec 24, 2025
R

broadinstitute /Tangram

Star354

Spatial alignment of single cell transcriptomic data.

computational-biology gene-expression scrna-seq spatial-data visium snrna-seq

UpdatedJul 1, 2025
Jupyter Notebook

scRNA-tools /scRNA-tools

Star338

Table of software for the analysis of single-cell RNA-seq data.

rna-seq database tools software scrna-seq single-cell single-cell-rna-seq

UpdatedFeb 20, 2026
R

theislab /scgen

Star335

Single cell perturbation prediction

bioinformatics deep-learning generative-model scrna-seq transcriptomics single-cell single-cell-genomics

UpdatedDec 5, 2024
Python

genecell /single-cell-papers-with-code

Star303

Papers with code for single cell related papers

reproducible-research reproducible-science scrna-seq single-cell single-cell-rna-seq single-cell-atac-seq single-cell-omics scrna-seq-analysis paper-with-code

UpdatedJan 10, 2026

liulab-dfci /MAESTRO

Star301

Single-cell Transcriptome and Regulome Analysis Pipeline

transcription-factors epigenetics scrna-seq snakemake-workflows scatac-seq gene-regulatory-networks

UpdatedMar 6, 2023
C

dpeerlab /Palantir

Star296

Single cell trajectory detection

markov-chain dimensionality-reduction scrna-seq trajectory-generation diffusion-maps differentiation manifold-learning single-cell-genomics cell-fate-transitions scrna-seq-analysis

UpdatedFeb 14, 2026
Jupyter Notebook

samuel-marsh /scCustomize

Star289

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

visualization ggplot2 customization scrna-seq single-cell single-cell-genomics single-cell-rna-seq seurat

UpdatedFeb 18, 2026
R

scverse /muon

Star262

muon is a multimodal omics Python framework

muon scrna-seq multi-omics multimodal-data cite-seq scanpy scatac-seq anndata multimodal-omics-analysis mudata scverse

UpdatedJan 19, 2026
Python

kharchenkolab /pagoda2

Star246

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

scrna-seq transcriptomics single-cell single-cell-rna-seq

UpdatedAug 18, 2025
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scrna-seq

Here are 504 public repositories matching this topic...

scverse /scvi-tools

COMBINE-lab /salmon

mdozmorov /scRNA-seq_notes

chanzuckerberg /cellxgene

hemberg-lab /scRNA.seq.course

zhanghao-njmu /SCP

immunogenomics /harmony

aristoteleo /dynamo-release