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 check the quality of Scanpy, Seurat, and CellRanger files.
More information on the read the doc page
Summary
Powered by nextflow, checkatlas can be ran in one command line:
checkatlas run search_folder/
The checkatlas workflow start with a fast crawl through your working directory. It detects Seurat (.rds), Scanpy (.h5ad) or cellranger (.h5) atlas files.
Then, it goes 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)
All tables and figs are saved in the checkatlas_files folder in your search folder.
A single html report is produced, using MultiQC, in checkatlas_files/Checkatlas-MultiQC.html.
Examples
-
Evaluate and compare different scanpy atlases: Example 1
-
Evaluate different version of one atlas: Example 2
-
Evaluate Scanpy, Seurat and CellRanger objects in your folder: Example 3
-
Evaluate an integrated Scanpy atlas with the corresponding raw CellRanger atlases: Example 4
-
Evaluate different Cellranger atlases with multiple chemistry version and cellranger version: Example 5
Installation
PyPi
The checkatlas python module can be downloaded with PyPi
pip install checkatlas
To benefit from the jax optimization of metrics you should install the version corresponding to your hardware
pip install checkatlas[cpu] → CPU-only JAX
pip install checkatlas[cuda13] → NVIDIA CUDA 13
pip install checkatlas[tpu] → Google Cloud TPU
Conda
conda install bioconda::checkatlas
Docker
docker pull quay.io/biocontainers/checkatlas
R install (obsolete for now)
Finally, checkatlas comes with rpy2 to perform the interface between python and R. But, it does not automatically install Seurat. So if you want to screen Seurat atlases you need to perfrom this last installation
% R
> install.packages('Seurat')
> library(Seurat)
Development
This project is in a very early development phase. All helpers are welcome. Please contact us or submit an issue.
Read the CONTRIBUTING.md file.
Checkatlas has two repositories:
It has a module on MultiQC
The checkatlas package is available on PyPI
The bioconda recipe has been submitted
Project developed thanks to the project template : (https://github.com/rochacbruno/python-project-template/)
1 maintainer
Metadata
1 maintainer
Release files for checkatlas 0.8.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| checkatlas-0.8.2.tar.gz | 130.3 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| checkatlas-0.8.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 308.1 kB
Release files / checkatlas-0.8.2.tar.gz
| Download URL | checkatlas-0.8.2.tar.gz |
|---|---|
| Size | 130.3 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
cf690b2db057273d79d05d81a4c8671aec97848f8d73081f807a9eb7d64ff7d7
|
|
BLAKE2b-256 checksum How to use checksums |
06dc4bfb0b60616631d4b046c9eaabec17af17ca4439f16811742d5d3ae9d0c0
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.13.12
|
Release files / checkatlas-0.8.2-py3-none-any.whl
| Download URL | checkatlas-0.8.2-py3-none-any.whl |
|---|---|
| Size | 177.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
7ab99e784acadc8327b198da017cf212d82154cd3b91ba5230f2a63979d25b7c
|
|
BLAKE2b-256 checksum How to use checksums |
d180741aa3ebc3522639e29a595aa07a4bc51d335f83734fd6270f273bc98c39
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.13.12
|
Security for checkatlas 0.8.2
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
