Awesome checkatlas created by becavin-lab
Project description
checkatlas
Awesome checkatlas created by becavin-lab
Summary
-
Parse Scanpy, Seurat and CellRanger objects
CheckAtlas should be able to load : .rds, .h5 and .h5ad corresponding to single-cell experiment. Need to implement :
- automatic conversion of Seurat object to Scanpy with SeuratDisk
- Rapid check-up of files to see if a Seurat or Scanpy can be found
- Automatic search in Scanpy files of key information = raw data, normalized data, integrated data, reductions, layers, assays, metadatas, etc...
-
Create checkatlas summary files
Go through all Scanpy files and extract summary information. We won't to extract :
- All basic QC (nRNA, nFeature, ratio_mito)
- General information (nbcells, nbgenes, nblayers)
- All elements in scanpy objects (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
Examples
-
Evaluate and compare different atlases: https://github.com/becavin-lab/checkatlas/blob/3a4f88e94716c09a3b9c86010f570743a5855461/examples/Atlas_comparison.ipynb
-
Evaluate different version of your atlas: https://github.com/becavin-lab/checkatlas/blob/3a4f88e94716c09a3b9c86010f570743a5855461/examples/Version_comparison.ipynb
-
Explore Scanpy, Seurat and CellRanger objects in your folder: https://github.com/becavin-lab/checkatlas/blob/main/examples/AtlasType_comparison.ipynb
Install it from PyPI
pip install checkatlas
Usage
from checkatlas import checkatlas
checkatlas.run(path, atlas_list, multithread, n_cpus)
$ cd your_search_folder/
$ python -m checkatlas .
#or
$ checkatlas .
Development
Read the CONTRIBUTING.md file.
Project developed thanks to the project template : (https://github.com/rochacbruno/python-project-template/)
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for checkatlas-0.0.1-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | e8f14453bee87e193439717c5bc6ca1d08f65a8a21248552ff5ec072c1b0cade |
|
MD5 | 99db07b1d5850c1c824b7aef9722bdbb |
|
BLAKE2b-256 | 9332977d4a0c843089da817ac62c04dc545b9d23d443d4294b1457efb455d2a6 |