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vineetbansal authored Jan 8, 2025
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[![Coverage Status](https://coveralls.io/repos/github/raphael-group/paste3/badge.svg?branch=main)](https://coveralls.io/github/raphael-group/paste3?branch=main)
[![Docs](https://github.com/raphael-group/paste3/actions/workflows/docs.yml/badge.svg)](https://raphael-group.github.io/paste3/)

<video src="https://github.com/user-attachments/assets/977c05c0-4c45-4d21-9302-dfe23800937e"/>


# Paste 3

**Paste 3** (Paste + Paste 2) is a Python package and NAPARI plugin that
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*Alignment and integration of spatial transcriptomics data.*
**Nat Methods**, 19, 567–575 (2022).

[Read the publication](https://doi.org/10.1038/s41592-022-01459-6)
[Read the publication](https://doi.org/10.1038/s41592-022-01459-6)
[Original PASTE code](https://github.com/raphael-group/paste)

---
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**Liu X, Zeira R, Raphael BJ.**
*Partial alignment of multislice spatially resolved transcriptomics data.*
**Genome Res.** 2023 Jul; 33(7):1124-1132.
[Read the publication](https://doi.org/10.1101/gr.277670.123)
[Read the publication](https://doi.org/10.1101/gr.277670.123)
[Original PASTE2 code](https://github.com/raphael-group/paste2)

The motivation behind PASTE3 is to provide a NAPARI plugin
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and then select one of the two modes of PASTE3 operations
(`Plugins->Paste3->Center Align` or `Plugins->Paste3->Pairwise Align`).

With the default parameters, alignment should take a couple of minutes, though
Your own datasets can be used if they're in the .h5ad format, with each file denoting a single
slice. With the default parameters, alignment should take a couple of minutes, though
you have the option of changing these to suit your needs.

<video src="https://github.com/user-attachments/assets/a527aa12-190e-46ed-a843-4cc10f8146ce"/>

If you intend to use PASTE3 programmatically in your Python code, follow along
the [Getting Started](https://raphael-group.github.io/paste3/notebooks/paste_tutorial.html)
tutorial.

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