PyPairs - A python scRNA-Seq classifier
This is a python-reimplementation of the Pairs algorithm as described by A. Scialdone et. al. (2015). Original Paper available under: https://doi.org/10.1016/j.ymeth.2015.06.021
A supervided maschine learning algorithm aiming to classify single cells based on their transcriptomic signal. Initially created to predict cell cycle phase from scRNA-Seq data, this algorithm can be used for various applications.
Build to be fully compatible with Scanpy. For more details see the full documentation.
Getting Started
Note: Version 3 still under development.
Installation
This package is hosted at PyPi ( https://pypi.org/project/pypairs/ ) and can be installed on any system running Python3 via pip with:
pip install pypairs
Alternatively, pypairs can be installed using Conda (most easily obtained via the Miniconda Python distribution:
conda install -c bioconda pypairs
Minimal Example
Assuming you have two scRNA count files (csv, columns = samples, rows = genes) and one annotation file (csv, no header, two rows: “gene, class”) a minimal example would look like this
from pypairs import pairs, datasets
# Load samples from the oscope scRNA-Seq dataset with known cell cycle
training_data = datasets.leng15(mode='sorted')
# Run sandbag() to identify marker pairs
marker_pairs = pairs.sandbag(training_data, fraction=0.6)
# Load samples from the oscope scRNA-Seq dataset without known cell cycle
testing_data = datasets.leng15(mode='unsorted')
# Run cyclone() score and predict cell cycle classes
result = pairs.cyclone(testing_data, marker_pairs)
# Further downstream analysis
print(result)Core Dependencies
License
This project is licensed under the BSD 3-Clause License - see the LICENSE file for details
1 maintainer
Metadata
1 maintainer
Release files for pypairs 3.0.7
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pypairs-3.0.7.tar.gz | 39.9 MB | Details |
Release files / pypairs-3.0.7.tar.gz
| Download URL | pypairs-3.0.7.tar.gz |
|---|---|
| Size | 39.9 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
4ba26d487416f67d95f3e393037b8321a87adb06df4e2417fd7fb9c3b9256b47
|
|
BLAKE2b-256 checksum How to use checksums |
449a35b6eb1218e39cec4f3d2edb9da9dd2422e19123e1e7d05ad5eca98b8bcc
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/1.12.1 pkginfo/1.5.0.1 requests/2.21.0 setuptools/40.7.1 requests-toolbelt/0.9.1 tqdm/4.30.0 CPython/3.6.3
|
