Panpipes - multimodal single cell pipelines

Panpipes: a pipeline for multiomic single-cell data analysis
Fabiola Curion, Charlotte Rich-Griffin, Devika Agarwal, Sarah Ouologuem, Tom Thomas, 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

how does panpipes work

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

flowchart overview of panpipes single cell pipelines

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