Panpipes - multimodal single cell pipelines
Project description
Panpipes - multimodal single cell pipelines
Created and Maintained by Charlotte Rich-Griffin and Fabiola Curion
Additional contributors: Devika Agarwal and Tom Thomas
See out 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 pipelines use cgat-core pipeline software
Available pipelines:
- "ingest" : for the ingestion of data and computation of QC metrics'
- "preprocess" : for filtering and normalising of each modality
- "integration" : integrate and batch correction using single and multimodal methods
- "clustering" : cell clustering on single modalities
- "refmap" : transfer scvi-tools models from published data to your data
- "vis" : visualise metrics from other pipelines in context of experiment metadata
Installation and configuration
See installation instructions here
Oxford BMRC Rescomp users find additional advice in docs/installation_rescomp
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