checkatlas 0.3.0

One liner tool to check the quality of your single-cell atlases.

CheckAtlas is a one liner tool to check the quality of your single-cell atlases. For every atlas, it produces the quality control tables and figures which can be then processed by multiqc. CheckAtlas is able to load Scanpy, Seurat, and CellRanger files.

Summary

Parse Scanpy, Seurat and CellRanger objects

The checkatlas pipeline start with a fast crawl through your working directory. It detects Seurat (.rds), Scanpy (.h5ad) or cellranger (.h5) atlas files.

Create checkatlas summary files

Go through all atlas files and produce summary information:

• All basic QC (nRNA, nFeature, ratio_mito)
• General information (nbcells, nbgenes, nblayers)
• All elements in atlas files (obs, obsm, uns, var, varm)
• Reductions (pca, umap, tsne)
• All metrics (clustering, annotation, dimreduction, specificity)

Parse checkatlas files in MultiQC

Update MultiQC project to add checkatlas parsing. Dev project in: https://github.com/becavin-lab/MultiQC/tree/checkatlas

https://checkatlas.readthedocs.io/en/latest/

Examples

1. Evaluate and compare different atlases: https://github.com/becavin-lab/checkatlas/blob/3a4f88e94716c09a3b9c86010f570743a5855461/examples/Atlas_comparison.ipynb

https://checkatlas.readthedocs.io/en/stable/CheckAtlas_example_1/CheckAtlas_example_1.html

2. Evaluate different version of your atlas: https://github.com/becavin-lab/checkatlas/blob/3a4f88e94716c09a3b9c86010f570743a5855461/examples/Version_comparison.ipynb

https://checkatlas.readthedocs.io/en/stable/CheckAtlas_example_2/CheckAtlas_example_2.html

3. Explore Scanpy, Seurat and CellRanger objects in your folder: https://github.com/becavin-lab/checkatlas/blob/main/examples/AtlasType_comparison.ipynb

https://checkatlas.readthedocs.io/en/stable/CheckAtlas_example_3/CheckAtlas_example_3.html

Installation

CheckAtlas can be downloaded from PyPI. However, the project is in an early development phase. We strongly recommend to use the developmental version.

Install checkatlas development version

git clone [e-mail]:becavin-lab/checkatlas.git
pip install checkatlas/.

Install MultiQC with checkatlas file management. This version of MultiQC is available at checkatlas branch of github.com:becavin-lab/MultiQC.

git clone [e-mail]:becavin-lab/MultiQC.git
cd MultiQC/
git checkout checkatlas
pip install .

Install it from PyPI

pip install checkatlas

Install Seurat

To be able to manage seurat file, rpy2 should have Seurat installed. The easiest way is to put all checkatlas requirements in a conda environment and add r-seurat.

conda create -n checkatlas python=3.9
pip install checkatlas
conda install -c bioconda r-seurat

Or, open R in checkatlas environment (the one where you ran 'pip install') and install Seurat.

% R
> install.packages('Seurat')
> library(Seurat)

Usage

The one liner way to run checkatlas is the following:

$ cd your_search_folder/
$ python -m checkatlas .
#or
$ checkatlas .

Or run it inside your python workflow.

from checkatlas import checkatlas
checkatlas.run(path, atlas_list, multithread, n_cpus)

Development

Read the CONTRIBUTING.md file.

Project developed thanks to the project template : (https://github.com/rochacbruno/python-project-template/)