| Name | paste2 JSON |
| Version |
1.0.1
JSON |
| download |
| home_page | |
| Summary | Probabilistic Alignment of Spatial Transcriptomics Experiments v.2 |
| upload_time | 2023-12-26 21:17:52 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.8 |
| license | BSD 3-Clause License Copyright (c) 2023, Princeton University Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
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| requirements |
No requirements were recorded.
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# PASTE2
PASTE2, the extension of PASTE, is a method for partial alignment and 3D reconstruction of spatial transcriptomics slices when they do not fully overlap in space.
There are three main functions:
1. `src/paste2/PASTE2/partial_pairwise_align`: Given a pair of ST slices and their overlap percentage, find a partial alignment matrix. Note: In a multi-sample dataset, partial_pairwise_align should be called on each pair of adjacent slices separately.
2. `src/paste2/model_selection/select_overlap_fraction`: Decide the overlap percentage (s parameter of partial_pairwise_align) between two input ST slices. Note: In a multi-sample dataset, each pair of adjacent slices could have a different overlap percentage, hence each pair of adjacent slices might have a different estimate of s to pass to partial_pairwise_align.
3. `src/paste2/projection/partial_stack_slices_pairwise`: Given a sequence of consecutive ST slices and the partial alignments between them, project all slices onto the same 2D coordinate system. 3D reconstruction can be done by assiging a z-value to each slice.
Additionally, `src/paste2/PASTE2/partial_pairwise_align_histology` uses both gene expression and histological image information for computing the partial alignment matrix.
## Installation
PASTE2 is available on PyPI at https://pypi.org/project/paste2/. To install PASTE2, run `pip install paste2`.
## Quick Start
We included a tutorial in this repo (`tutorial.ipynb`). The tutorial should cover the basics you need to run PASTE2 on your own dataset. Additionally, the documentation of each function is in the source code.
## Contact
If you encounter any problem running the software, please contact Xinhao Liu at xl5434@princeton.edu
## Reference
Liu, X., Zeira, R., & Raphael, B. J. (2023). Partial alignment of multislice spatially resolved transcriptomics data. Genome Research, 33(7), 1124-1132.
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"description": "# PASTE2\n\n\nPASTE2, the extension of PASTE, is a method for partial alignment and 3D reconstruction of spatial transcriptomics slices when they do not fully overlap in space. \n\nThere are three main functions:\n1. `src/paste2/PASTE2/partial_pairwise_align`: Given a pair of ST slices and their overlap percentage, find a partial alignment matrix. Note: In a multi-sample dataset, partial_pairwise_align should be called on each pair of adjacent slices separately.\n2. `src/paste2/model_selection/select_overlap_fraction`: Decide the overlap percentage (s parameter of partial_pairwise_align) between two input ST slices. Note: In a multi-sample dataset, each pair of adjacent slices could have a different overlap percentage, hence each pair of adjacent slices might have a different estimate of s to pass to partial_pairwise_align.\n3. `src/paste2/projection/partial_stack_slices_pairwise`: Given a sequence of consecutive ST slices and the partial alignments between them, project all slices onto the same 2D coordinate system. 3D reconstruction can be done by assiging a z-value to each slice.\n\nAdditionally, `src/paste2/PASTE2/partial_pairwise_align_histology` uses both gene expression and histological image information for computing the partial alignment matrix.\n\n\n\n## Installation\nPASTE2 is available on PyPI at https://pypi.org/project/paste2/. To install PASTE2, run `pip install paste2`. \n\n## Quick Start\nWe included a tutorial in this repo (`tutorial.ipynb`). The tutorial should cover the basics you need to run PASTE2 on your own dataset. Additionally, the documentation of each function is in the source code.\n\n## Contact\nIf you encounter any problem running the software, please contact Xinhao Liu at xl5434@princeton.edu\n\n## Reference\nLiu, X., Zeira, R., & Raphael, B. J. (2023). Partial alignment of multislice spatially resolved transcriptomics data. Genome Research, 33(7), 1124-1132.",
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