One liner tool to check the quality of your single-cell atlases.
Project description
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
Example 1 - Evaluate and compare heterogenous scanpy atlases
Evaluate and compare different atlases:
Example 2 - Evaluate different version of the same atlas
Evaluate different version of your atlas:
Example 3 - Evaluate Scanpy, Seurat and CellRanger atlases
Evaluate Scanpy, Seurat and CellRanger objects in your folder:
Example 4 - Evaluate post-process and raw atlases
Evaluate an integrated Scanpy atlas with the corresponding raw CellRanger atlases:
Example 5 - Avaluate different cellranger version atlases
Evaluate different Cellranger atlases with multiple chemistry version and cellranger version:
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 git@github.com: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 git@github.com: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/)
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