panpipes 0.4.0

Panpipes - multimodal single cell pipelines

Panpipes - multimodal single cell pipelines

Created and Maintained by Charlotte Rich-Griffin and Fabiola Curion
Additional contributors: Sarah Ouologuem, Devika Agarwal and Tom Thomas

See our documentation and our preprint:
Panpipes: a pipeline for multiomic single-cell data analysis
Charlotte Rich-Griffin*, Fabiola Curion*, Tom Thomas, Devika Agarwal, Fabian J. Theis, Calliope A. Dendrou.
bioRxiv 2023.03.11.532085;
doi: https://doi.org/10.1101/2023.03.11.532085

Introduction

These workflows use cgat-core pipeline software

Available workflows:

1. "ingest" : for the ingestion of data and computation of QC metrics
2. "preprocess" : for filtering and normalising of each modality
3. "integration" : integrate and batch correction using single and multimodal methods
4. "clustering" : cell clustering on single modalities
5. "refmap" : transfer scvi-tools models from published data to your data
6. "vis" : visualise metrics from other pipelines in context of experiment metadata
7. "qc_spatial": for the ingestion of Spatial Transcriptomics data (vizgen, visium) and computation of QC metrics
8. "preprocess_spatial" : for filtering and normalising of ST data
9. "deconvolution": for the cell type deconvolution of ST slides

Installation and configuration

See installation instructions here

Oxford BMRC Rescomp users find additional advice in docs/installation_rescomp

Releases

panpipes v0.4.0 is out now!

The ingest workflow now expects different headers for the RNA and Protein modalities. Check the example submission file and the documentation for more detailed instructions.