COLLECTION 02 / Explore cell states

Single-cell Analysis.

Find public single-cell data and the R or Python tools that can take an expression matrix further.

Where to start

If you are exploring a published atlas, start with a browser. If you are analyzing your own counts, choose a tool that matches your data format and environment, and keep biological replicates separate in statistical comparisons.

Tools in this collection

41 EDITORIAL LISTINGS

Open source

Scanpy

Move from a single-cell expression matrix to quality checks, clusters, and exploratory plots in Python.

Single-cell AnalysisPython package

Open source

Seurat

Explore single-cell expression data in R, from initial filtering and clustering to comparisons across samples.

Single-cell AnalysisR package

Free

CZ CELLxGENE Discover

Browse public single-cell datasets, inspect gene expression and cell annotations, or download data for follow-up analysis.

Single-cell AnalysisPublic data portal

Open source

scater

Inspect single-cell expression data with quality-control summaries, embeddings, and plots built around Bioconductor objects.

Single-cell AnalysisR package

Open source

SingleCellExperiment

Store expression matrices, gene and cell metadata, and embedding coordinates together in a standard R object.

Single-cell AnalysisR package

Open source

iSEE

Explore a prepared experiment in a browser with linked scatter plots, metadata tables, and expression views.

Single-cell AnalysisR / Shiny app

Open source

scDblFinder

Flag likely doublets, where a capture event contains more than one cell, before downstream interpretation.

Single-cell AnalysisR package

Open source

CellRank

Estimate candidate cell-state transitions and fate probabilities from processed single-cell observations.

Single-cell AnalysisPython package

Open source

AnnData

Keep a cell-by-feature matrix, annotations, and embeddings aligned in one object.

Single-cell AnalysisPython package

Open source

MuData

Organize modality-specific matrices and shared annotations together in a single container.

Single-cell AnalysisPython package

Open source

scvi-tools

Fit probabilistic models for tasks such as learning shared expression embeddings or transferring labels.

Single-cell AnalysisPython package

Open source

Squidpy

Summarize the arrangement of cells or spots in tissue with spatial neighbor graphs and coordinate-aware plots.

Single-cell AnalysisPython package

Open source

SpatialData

Keep expression tables, images, labels, and points in a common spatial data model.

Single-cell AnalysisPython package

Open source

Muon

Process measurements from separate modalities and combine their neighborhood information for exploratory analysis.

Single-cell AnalysisPython package

Open source

CellTypist

Assign provisional cell-type labels to RNA expression profiles using a selected pretrained classifier.

Single-cell AnalysisPython package

Open source

RAPIDS-singlecell

Run supported single-cell preprocessing and analysis steps on a GPU.

Single-cell AnalysisPython package

Open source

Cirrocumulus

Browse large expression datasets with linked embeddings, expression plots, and cluster composition views.

Single-cell AnalysisWeb visualization app

Open source

scVelo

Estimate RNA velocity to examine candidate directions of change among observed cell states.

Single-cell AnalysisPython package

Open source

DropletUtils

Read common droplet data formats and distinguish candidate cells from background droplets.

Single-cell AnalysisR package

Open source

batchelor

Reduce batch differences between expression datasets with methods including mutual nearest-neighbor correction.

Single-cell AnalysisR package

Open source

SingleR

Compare single-cell expression profiles with labeled references to suggest cell identities.

Single-cell AnalysisR package

Open source

celldex

Retrieve labeled expression references for human and mouse cell annotation.

Single-cell AnalysisR package

Open source

zellkonverter

Exchange H5AD expression data between Python's AnnData format and Bioconductor's SingleCellExperiment class.

Single-cell AnalysisR package

Open source

muscat

Test expression differences within annotated cell populations across samples, including pseudobulk analysis.

Single-cell AnalysisR package

Open source

miloR

Test for differences in cell abundance across graph neighborhoods without relying on a single partition into clusters.

Single-cell AnalysisR package

Open source

slingshot

Fit candidate branching trajectories through clusters and order cells along those trajectories.

Single-cell AnalysisR package

Open source

tradeSeq

Fit smooth gene expression trends along inferred trajectories and compare patterns between branches.

Single-cell AnalysisR package

Open source

dreamlet

Compare expression by cell type across cohorts, including designs with repeated samples.

Single-cell AnalysisR package

Open source

dittoSeq

Create configurable plots for expression, composition, and embeddings with colorblind-friendly palette options.

Single-cell AnalysisR package

Open source

Nebulosa

Overlay gene-weighted density on an embedding to show where expression from one or more features is concentrated.

Single-cell AnalysisR package

Open source

UCell

Score individual cells against predefined gene sets using expression ranks.

Single-cell AnalysisR package

Open source

SpatialExperiment

Keep spatial coordinates and image metadata aligned with expression assays in a Bioconductor object.

Single-cell AnalysisR package

Open source

scRNAseq

Load selected published single-cell count datasets and annotations into ready-to-analyze R objects.

Single-cell AnalysisR package

Open source

sctransform

Normalize UMI expression with a model that accounts for sequencing depth and stabilizes variation across genes.

Single-cell AnalysisR package

Open source

Harmony

Align single-cell datasets in a low-dimensional space while accounting for selected batch variables.

Single-cell AnalysisR package

Open source

scrapper

Use R interfaces to compiled routines for single-cell quality control, clustering, and marker summaries.

Single-cell AnalysisR package

Free

Human Cell Atlas Data Explorer

Find Human Cell Atlas projects and inspect their sample, tissue, and file metadata.

Single-cell AnalysisPublic data portal

Free

Broad Single Cell Portal

Explore public studies through interactive plots and retrieve the files their owners have made available.

Single-cell AnalysisPublic data portal

Free

EMBL-EBI Single Cell Expression Atlas

Search single-cell expression studies across species and inspect gene expression patterns within individual experiments.

Single-cell AnalysisPublic data portal

Free

UCSC Cell Browser

Open hosted datasets and color cell embeddings by gene expression or sample metadata.

Single-cell AnalysisPublic data portal

Free

Allen Brain Cell Atlas

Browse reference brain cell expression and spatial data to compare annotated neural populations.

Single-cell AnalysisPublic data portal