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Workflow shortcuts:🧬 Protein Structure 💊 Molecular Design 🧫 Single-Cell 🔬 Genomics 📸 Cryo-EM 🔓 Open Source

26 matching products · 26 products on page 1. Filters search the whole catalog.

Single-Cell & Spatial Biology

Single-Cell Batch CorrectionOpen Source

Harmony

Software Library (R / Python) · Open Source

Fast, sensitive and flexible integration of single-cell data

Broad Institute / Harvard Medical School (Raychaudhuri Lab)

GitHub ↗

Free Open Source

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Single-Cell & Spatial Biology

Spatial Omics Data InfrastructureOpen Source

SpatialData

Python Library · Open Source

Unified data framework and storage format for spatial multi-omics

scverse Consortium

Free Open Source

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Single-Cell & Spatial Biology

Cell-Cell CommunicationOpen Source

CellChat

R Software Package · Open Source

Inference and analysis of cell-cell communication networks from single-cell data

University of California, Irvine (Nie Lab)

GitHub ↗

Free Open Source

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Single-Cell & Spatial Biology

Single-Cell Processing Pipelines

Cell Ranger

Software Pipeline · Proprietary Freeware

The industry-standard analysis pipeline for Chromium single-cell sequencing

10x Genomics

Free to download for 10x Genomics data

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Single-Cell & Spatial Biology

Single-Cell Atlas MappingOpen Source

scArches

Open Source Software · Open Source

Single-cell architectural surgery for reference atlas mapping without data sharing

Helmholtz Munich (Theis Lab)

GitHub ↗

Free Open Source

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Single-cell, Spatial & Cytometry

Single-cell Analysis

muon

Supporting software · Public code / project terms

Multimodal omics data handling and analysis

scverse / muon contributors

GitHub ↗

See project terms; compute costs may apply

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Single-cell, Spatial & Cytometry

Perturbation Models

Pertpy

Research software / framework · Public code / project terms

Framework for single-cell perturbation analysis

scverse / Pertpy contributors

GitHub ↗

See project terms; compute costs may apply

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Single-cell, Spatial & Cytometry

Spatial AnalysisAcademic

SPArrOW

Supporting software · Public code / project terms

Interactive pipeline for spatial transcriptomics analysis

Saeys laboratory

GitHub ↗

See project terms; compute costs may apply

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Single-cell, Spatial & Cytometry

Single-cell Models

CellPLM

Research software / model · Public code / project terms

Cell language modeling with cell-cell context

OmicsML / CellPLM authors

GitHub ↗

See project terms; compute costs may apply

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Single-cell, Spatial & Cytometry

Single-cell Models

Geneformer

Research software / model · Public code / project terms

Transformer representations of single-cell transcriptomes

Theodoris laboratory and collaborators

See project terms; compute costs may apply

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Single-cell, Spatial & Cytometry

Spatial Analysis

Giotto Suite

Supporting software · Public code / project terms

Spatial multi-omics processing, analysis and visualization

Dries laboratory and collaborators

See project terms; compute costs may apply

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Single-cell, Spatial & Cytometry

Cell Annotation

scBERT

Research software / model · Public code / project terms

Pretrained language modeling for cell-type annotation

scBERT research authors

GitHub ↗

See project terms; compute costs may apply

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Single-cell, Spatial & Cytometry

Single-cell Analysis

scVelo

Research software / model · Public code / project terms

RNA velocity and cellular dynamics analysis

Theis laboratory / scVelo contributors

GitHub ↗

See project terms; compute costs may apply

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Single-cell, Spatial & Cytometry

Single-cell Models

Universal Cell Embeddings

Research software / model · Public code / project terms

Foundation-model embeddings for single-cell expression

Stanford SNAP / UCE contributors

GitHub ↗

See project terms; compute costs may apply

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Single-cell, Spatial & Cytometry

Spatial Analysis

cell2location

Research software / model · Public code

Bayesian mapping of cell types in spatial transcriptomics

cell2location contributors

See project licence and access terms

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Single-cell, Spatial & Cytometry

Cell Annotation

CellTypist

Research software / model · Public code

Semi-automatic cell type classification

Teichmann Lab / CellTypist contributors

GitHub ↗

See project licence and access terms

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Single-cell, Spatial & Cytometry

Perturbation Models

GEARS

Research software / model · Public code

Predicting transcriptional perturbation outcomes

Stanford SNAP / GEARS authors

GitHub ↗

See project licence and access terms

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Single-cell, Spatial & Cytometry

Cytometry

openCyto

Supporting software · Public code

Reproducible automated cytometry gating

openCyto contributors

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Single-cell, Spatial & Cytometry

Cytometry

PhenoGraph

Research software / model · Public code

Subpopulation detection in single-cell data

Pe’er Lab / PhenoGraph contributors

GitHub ↗

See project licence and access terms

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Single-cell, Spatial & Cytometry

Single-cell Analysis

Scanpy

Supporting software · Public code

Python toolkit for single-cell analysis

scverse / Scanpy contributors

See project licence and access terms

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Single-cell, Spatial & Cytometry

Spatial Analysis

Squidpy

Supporting software · Public code

Spatial single-cell analysis in Python

scverse / Squidpy contributors

See project licence and access terms

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Single-cell, Spatial & Cytometry

Spatial Analysis

Tangram

Research software / model · Public code

Mapping single-cell expression into space

Broad Institute / Tangram contributors

GitHub ↗

See project licence and access terms

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Single-cell, Spatial & Cytometry

Single-cell Analysis

Seurat

Supporting software · Public code

R toolkit for single-cell genomics

Satija Lab

See project licence and access terms

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Single-cell, Spatial & Cytometry

Cytometry

FlowSOM

Research software / model · Public code

Self-organizing maps for cytometry

FlowSOM contributors

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Single-cell, Spatial & Cytometry

Single-cell Models

scGPT

Research software / model · Public research code

Foundation models for single-cell omics

Bo Wang Lab

GitHub ↗

See access and licence terms

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Single-cell, Spatial & Cytometry

Single-cell Models

scvi-tools

Research software / model · Public code

Probabilistic models for single-cell analysis

scverse / scvi-tools contributors

See access and licence terms

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