Package Health Score

72 / 100

security
No known security issues
popularity
Small
maintenance
Inactive
community
Active

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Popularity

Small

GitHub Stars: 42.24K
Forks: 17.42K
Contributors: 420

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package stereoAlign, we found that it has been starred 42,239 times.

Security

No known security issues

Security and license risk for latest version

Release Date: Aug 24, 2023
Direct Vulnerabilities: 0
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Indirect Vulnerabilities: 0
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License Risk: 0
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All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

BSD-3-Clause

Security Policy

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Maintenance

Inactive

Commit Frequency

Open Issues: 3.65K
Open PR: 148
Last Release: 11 months ago
Last Commit: 2 months ago

Further analysis of the maintenance status of stereoAlign based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Inactive.

We found that stereoAlign demonstrates a positive version release cadence with at least one new version released in the past 12 months.

In the past month we didn't find any pull request activity or change in issues status has been detected for the GitHub repository.

Community

Active

Readme: Yes
Contributing.md: No
Code of Conduct: Yes
Contributors: 420
Funding: Yes

A good and healthy external contribution signal for stereoAlign project, which invites more than one hundred open source maintainers to collaborate on the repository.

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Package

Python Versions Compatibility: >=3.8

Age: 12 months
Latest Release: 11 months ago
Dependencies: 16 Direct
Versions: 3
Maintainers: 1
Wheels: OS Independent

Readme

A toolkit for data integration

Behold, a magnificent toolkit emerges, designed to seamlessly integrate the vast realm of data in the realm of single-cell genomics. Within its hallowed digital confines, this toolkit bestows upon researchers the power to harmoniously merge and analyze the intricate tapestry of cellular information. Crafted with meticulous care, this toolkit embodies the epitome of elegance and efficiency. It serves as a conduit, enabling the synthesis of diverse datasets from single-cell genomics experiments, unlocking new realms of knowledge and understanding. The power of data integration within this toolkit extends beyond mere aggregation. It empowers researchers to unravel the intricate web of cellular interactions, uncovering hidden patterns, identifying novel cell types, and discerning the complex dynamics that govern cellular behavior. Through its refined algorithms and advanced statistical techniques, this toolkit illuminates the path towards deeper insights and discoveries. It refines and enhances the quality of data, mitigating confounding factors and removing noise, thus unveiling the true essence of the cellular landscape. As the sun sets on the horizon of single-cell genomics, this toolkit emerges as a guiding beacon, illuminating the path towards a more comprehensive understanding of cellular complexity. Embrace its power and unlock the secrets hidden within the realm of single-cell genomics.

Dependence

Install

The stereoAlign python package is available on Pypi and can be installed through

pip install stereoAlign

Import stereoAlign in python

import stereoAlign

We created the python package called stereoAlign that uses scanpy to streamline the integration of single-cell datasets and evaluate the results. The package contains several modules for preprocessing an anndata object, running integration methods and evaluating the resulting using a number of metrics. Functions for the data integration methods are in stereoAlign.alignment or for short stereoAlign.alg and metrics are under stereoAlign.metrics.

Tutorials

Quick Start https://stereoalign-tutorial.readthedocs.io/en/latest/index.html#

Integration Tools

This repository contains the code for the stereoAlign package for data integration tools.
This toolkit that is compared include:

Integration Method	Invoke	Output	Recommendation index	Describe	Language
`Harmony`	`stereoAlign.alg.harmony_alignment`	Embedding	*******	Leverage iterative clustering with maximum diversity for batch correction and integration.	Python / R
`Scanorama`	`stereoAlign.alg.scanorama_alignment`	Embedding	********	Leverage computer vision algorithms for panorama stitching matches for batch correction and integration.	Python
`scGEN`	`stereoAlign.alg.scgen_alignment`	Features	********	Use variational autoencoders to reduce the dimension of gene expression matrix, and apply extra label to batch correction and integrations.	Python
`scvi`	`stereoAlign.alg.scvi_alignment`	Embedding	********	Use variational autoencoders to batch correct and integrate.	Python
`MNN`	`stereoAlign.alg.mnn_alignment`	Features	**	Leverage mutual nearest neighbor for batch correction and integration.	Python
`BBKNN`	`stereoAlign.alg.bbknn_alignment`	Graph	*******	BBKNN taking each cell and identifying a (smaller) k nearest neighbours in each batch separately, and merged into a final neighbour list for the cell.	Python
`Combat`	`stereoAlign.alg.combat_alignment`	Features	*	Leverage empirical Bayesian model for batch correction and integration.	Python
`DESC`	`stereoAlign.alg.desc_alignment`	Embedding	**	DESC eventually eliminates batch effects by recurrent self-learning, as long as technological changes between batches are fewer than real biological variances.	Python
`PRECAST`		Embedding	********	PRECAST is a probabilistic model-based approach that integrates SRT datasets from multiple tissue slides.	R
`spatiAlign`	`stereoAlign.alg.spatialign_alignment`	Embedding / Features	*****	spatiAlign is an unsupervised across domain adapatation methods for SRT datasets batch correction and integration.	Python
`SCALEX`	`stereoAlign.alg.scalex_alignment`	Embedding	**	SCALEX leverage domain specific batch normalization for batch correction and integration.	Python

Metric

Metric Method	Invoke
ARI	`stereoAlign.metrics.cal_ari`
Graph connectivity	`stereoAlign.metrics.cal_graph_connectivity`
KBET	`stereoAlign.metrics.cal_kbet`
LISI	`stereoAlign.metrics.cal_lisi`
Silhouette	`stereoAlign.metrics.cal_silhouette`

Disclaimer

This is not an official product.

stereoAlign dependencies

bbknn desc h5py harmony-pytorch louvain matplotlib mnnpy numpy pandas python-igraph scanorama scanpy scgen scikit-learn scvi-tools tensorflow

FAQs

What is stereoAlign?

A toolkit package of data integration. Visit Snyk Advisor to see a full health score report for stereoAlign, including popularity, security, maintenance & community analysis.

Is stereoAlign popular?

The python package stereoAlign receives a total of 20 weekly downloads. As such, stereoAlign popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is stereoAlign well maintained?

We found indications that stereoAlign is an Inactive project. See the full package health analysis to learn more about the package maintenance status.

Is stereoAlign safe to use?

The python package stereoAlign was scanned for known vulnerabilities and missing license, and no issues were found. Thus the package was deemed as safe to use. See the full health analysis review.

Last updated on 27 July-2024, at 20:55 (UTC).

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stereoAlign

A toolkit package of data integration For more information about how to use this package see README

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Package

Readme

A toolkit for data integration

Dependence

Install

Tutorials

Integration Tools

Metric

Disclaimer

stereoAlign dependencies

FAQs

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Is stereoAlign safe to use?

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Readme

A toolkit for data integration

Dependence

Install

Tutorials

Integration Tools

Metric

Disclaimer

stereoAlign dependencies

FAQs

What is stereoAlign?

Is stereoAlign popular?

Is stereoAlign well maintained?

Is stereoAlign safe to use?

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Source Code

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