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atlas_protocol

Before you begin

Building a single-cell atlas

Merge datasets, harmonize annotations and metadata
Quality control and filtering
Cell-type annotation of “seed” datasets
Integrate data and perform doublet detection
Cell-type annotation

Downstream analysis

Differential gene expression
Compositional analysis
Functional analysis: PROGENy / DoRothEA / CytoSig
Cell-to-cell communication
Integration with bulk RNA-seq data
Next steps

Helper package documentation

API

About this project

Changelog
Contributing guide
References

.ipynb

Integrate data and perform doublet detection

Integrate data and perform doublet detection#

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Cell-type annotation

By Gregor Sturm

© Copyright 2023, Gregor Sturm..