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Merge current development branch#70

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mgbckr merged 99 commits intomasteryuqiyuqitan/SPACEc:masterfrom combined_updates_yuqiyuqiyuqitan/SPACEc:combined_updates_yuqiCopy head branch name to clipboardJan 27, 2025

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Commits

Commits on Oct 27, 2024

• Updating PPA and cn_map

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• Adding the new plot mask function

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Commits on Nov 5, 2024

• Fixing the figsize issue with the CN heatmap

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Commits on Nov 6, 2024

• Fixing the triangulation symmetry bug

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• Update filter interaction function to account for small populations of cell types that can shift the results

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Commits on Nov 7, 2024

• Fixing errors in last update

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Commits on Nov 10, 2024

• Update description of STELLAR notebook

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Commits on Nov 17, 2024

• Update 3_clustering.ipynb

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Commits on Nov 24, 2024

• Add interactive clustering + bug fixes

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• update setup file

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• Cleaning tools

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• Updating TM functions

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• formatting

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• update testing

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• fixes

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• updating tests

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• Update _general.py

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• Update __init__.py

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• Update __init__.py

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• updating distance permutation testing nb and filtering

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Commits on Dec 3, 2024

• Adding Notebook for clustering GUI

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• Update to make STELLAR less memory hungry

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Commits on Dec 8, 2024

• compatibility for tensorflow

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• fix

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• change back

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Commits on Dec 15, 2024

• adding install script for fast and easy install

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• Update README.md

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• Allow PPA to work with single cluster

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Commits on Dec 22, 2024

• Update install_spacec.sh

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• Add Spillover correction to SPACEc based on CellSeg compensation

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• Update _general.py

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• Update _general.py

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Commits on Dec 24, 2024

• Update README.md

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Commits on Dec 28, 2024

• fixing support for custom cellpose models

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• Adding custom cellpose model to run tests

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• Update test_1_cell_segmentation.py

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• Merge branch 'combined_updates_tim' of https://github.com/yuqiyuqitan/SPACEc into combined_updates_tim

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• fixing previous commit

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Commits on Dec 29, 2024

• Update install_spacec.sh

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Commits on Jan 2, 2025

• Small fix to make tests run (networkx < 3.4)

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• Make things pretty for pre-commit

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Commits on Jan 3, 2025

• Preparation for Apple Silicon builds

  

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• Fix pre-commit

  

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• Install libvips on Mac

  

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• Tox for macos build

  

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• Fix pre-commit

  

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• Try to fix missing openslide

  

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Commits on Jan 4, 2025

• Try to fix missing openslide

  

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• Update README.me

  

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• Tensorflow test

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• Tensorflow test

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• Tensorflow test

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• Tensorflow test on Ubuntu

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• Tensorflow test on Ubuntu

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• Add badges

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Commits on Jan 14, 2025

• updates

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• readme formatting

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• further updating readme

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• update typo

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Commits on Jan 20, 2025

• update the installation on readme, remove boxplot from filter_data and make the scatterplots optional, add docker files

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Commits on Jan 21, 2025

• Minor corrections of README.md

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• adding import for catplot to fix bug in clustering GUI

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• removing old chunk

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• Updating TM function

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• Update _general.py

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• Update README.md

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Commits on Jan 22, 2025

• Requirement testing

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• Fix pre-commit

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• Update README.md

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Commits on Jan 23, 2025

• Update SPACEc_cpu

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• Update SPACEc_gpu

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Commits on Jan 24, 2025

• Merge remote-tracking branch 'origin/combined_updates_tim_mgbckr' into combined_updates_yuqi

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• Dependency installation updates

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• Clean up

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• Test without env variable

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Commits on Jan 26, 2025

• Update install routine

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Commits on Jan 27, 2025

• Update install routine in README.md

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• Fix tox.ini

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