Metadata-Version: 2.1
Name: panpipes
Version: 1.1.0
Summary: Panpipes - multimodal single cell pipelines
Author: Charlotte Rich-Griffin, Fabiola Curion
Classifier: License :: OSI Approved :: BSD License
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: R
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: jax
Requires-Dist: jaxlib
Requires-Dist: apsw
Requires-Dist: bbknn
Requires-Dist: cgatcore
Requires-Dist: drmaa
Requires-Dist: gevent
Requires-Dist: harmonypy
Requires-Dist: mofapy2
Requires-Dist: muon
Requires-Dist: matplotlib
Requires-Dist: openpyxl
Requires-Dist: paramiko
Requires-Dist: pysam
Requires-Dist: pyyaml
Requires-Dist: ruffus
Requires-Dist: scanorama
Requires-Dist: scanpy
Requires-Dist: seaborn
Requires-Dist: leidenalg
Requires-Dist: louvain
Requires-Dist: scib
Requires-Dist: scib-metrics
Requires-Dist: scikit-misc
Requires-Dist: scirpy
Requires-Dist: scrublet
Requires-Dist: scvi-tools
Requires-Dist: sqlalchemy
Provides-Extra: dev
Requires-Dist: packaging; extra == "dev"
Requires-Dist: pytest; extra == "dev"
Requires-Dist: twine; extra == "dev"
Requires-Dist: build; extra == "dev"
Provides-Extra: notebook
Requires-Dist: jupyter; extra == "notebook"
Requires-Dist: jupyterlab; extra == "notebook"
Provides-Extra: spatial
Requires-Dist: jax==0.4.23; extra == "spatial"
Requires-Dist: jaxlib==0.4.23; extra == "spatial"
Requires-Dist: scvi-tools==1.0.4; extra == "spatial"
Requires-Dist: scipy==1.12.0; extra == "spatial"
Requires-Dist: squidpy; extra == "spatial"
Requires-Dist: cell2location; extra == "spatial"
Requires-Dist: tangram-sc; extra == "spatial"
Provides-Extra: refmap-old
Requires-Dist: scvi-tools; extra == "refmap-old"
Requires-Dist: pandas<2.0.0; extra == "refmap-old"
Requires-Dist: scib; extra == "refmap-old"

[![PyPI version](https://badge.fury.io/py/panpipes.svg)](https://badge.fury.io/py/panpipes)

# Panpipes - multimodal single cell pipelines

## Overview

Panpipes is a set of computational workflows designed to automate multimodal single-cell and spatial transcriptomic analyses by incorporating widely-used Python-based tools to perform quality control, preprocessing, integration, clustering, and reference mapping at scale.
Panpipes allows reliable and customisable analysis and evaluation of individual and integrated modalities, thereby empowering decision-making before downstream investigations.

**See our [documentation](https://panpipes-pipelines.readthedocs.io/en/latest/) and our [preprint](https://www.biorxiv.org/content/10.1101/2023.03.11.532085v2)**  

These workflows make use of [cgat-core](https://github.com/cgat-developers/cgat-core)

Available workflows:

1. "ingest" : Ingest data and compute quality control metrics
2. "preprocess" : Filter and normalize per modality
3. "integration" : Integrate and batch correct using single and multimodal methods
4. "clustering" : Cluster cells per modality
5. "refmap" : Map queries against reference datasets
6. "vis" : Visualize metrics from other pipelines in the context of experiment metadata
7. "qc_spatial" : Ingest spatial transcriptomics data (Vizgen, Visium) and compute quality control metrics
8. "preprocess_spatial" : Filtering and normalize spatial transcriptomics data
9. "deconvolution_spatial" : Deconvolve cell types of spatial transcriptomics slides

## Installation and configuration

For detailed installation instructions (including those for Apple Silicon machines), refer to the [installation instructions here](https://panpipes-pipelines.readthedocs.io/en/latest/install.html).

We recommend installing panpipes in a conda environment.
For that, we provide a minimal conda config file in `pipeline_env.yaml`.
First, clone this repository and navigate to the root directory of the repository:

```bash
git clone https://github.com/DendrouLab/panpipes.git
cd panpipes
```

Then, create the conda environment and install the nightly version of panpipes using the following command:

```bash
conda env create --file=pipeline_env.yaml 
conda activate pipeline_env
pip install -e .
```

Oxford BMRC Rescomp users find additional advice on the installation [here](https://github.com/DendrouLab/panpipes/blob/main/docs/installation_rescomp.md).

## Releases

Since `panpipes v0.4.0`, the `ingest` workflow expects different headers for the RNA and Protein modalities from the previous releases.
Check the example [submission file](https://github.com/DendrouLab/panpipes/blob/main/docs/usage/sample_file_qc_mm.md) and the [documentation](https://panpipes-pipelines.readthedocs.io/en/latest/usage/setup_for_qc_mm.html) for more detailed instructions.

## Citation

[Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis
Fabiola Curion, Charlotte Rich-Griffin, Devika Agarwal, Sarah Ouologuem, Tom Thomas, Fabian J. Theis, Calliope A. Dendrou
bioRxiv 2023.03.11.532085; doi: https://doi.org/10.1101/2023.03.11.532085](https://www.biorxiv.org/content/10.1101/2023.03.11.532085v2)

## Contributors

Created and Maintained by Charlotte Rich-Griffin and Fabiola Curion.
Additional contributors: Sarah Ouologuem, Devika Agarwal, Lilly May, Kevin Rue-Albrecht, Giulia Garcia, Lukas Heumos.
