Panpipes - multimodal single cell pipelines

Check out our paper:

Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis

Fabiola Curion, Charlotte Rich-Griffin, Devika Agarwal, Sarah Ouologuem, Kevin Rue-Albrecht, Lilly May, Giulia E. L. Garcia, Lukas Heumos, Tom Thomas, Wojciech Lason, David Sims, Fabian J. Theis & Calliope A. Dendrou

What is Panpipes?

Panpipes is a collection of cgat-core/ruffus pipelines to streamline the analysis of multi-modal single cell data. Panpipes supports any combination of the following single-cell modalities: scRNAseq, CITEseq, scV(D)Jseq, and scATACseq

Check out the installation and usage guidelines page for further information.

Available workflows for multimodal data:

1. Ingestion and Quality Control metrics generation : for the ingestion of data and computation of QC metrics

2. Preprocessing : for filtering and normalizing each modality

3. Integration: integrate and batch correction using single and multimodal methods

4. Clustering : cell clustering on single modalities

5. Reference Mapping (refmap) : transfer scvi-tools models from published data to your data

6. Visualization : visualize metrics from other pipelines in the context of experiment metadata

Available workflows for spatial data:

1. Ingesting spatial data : for the ingestion of spatial transcriptomics (ST) data (Vizgen, Visium) and computation of QC metrics

2. Preprocessing spatial data: for filtering and normalizing ST data

3. Deconvoluting spatial data : for the cell type deconvolution of ST slides

4. Clustering spatial data : for clustering ST data

Contents

• Installation of panpipes
• Usage guidelines
• Workflows
• Workflows configuration files
• Tutorials
• Releases
• Contributing to panpipes
• Contributors