panpipes 0.3.0

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 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:

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