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Add function for calculating niches#831

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LLehner wants to merge 89 commits intomainscverse/squidpy:mainfrom niche_definitionsscverse/squidpy:niche_definitionsCopy head branch name to clipboard

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Commits on May 27, 2024

• Add function for calculating niches

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• Update __init__.py

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• Merge branch 'main' into niche_definitions

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Commits on May 29, 2024

• Add function

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Commits on Jun 8, 2024

• Update

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• Merge branch 'niche_definitions' of https://github.com/scverse/squidpy into niche_definitions

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Commits on Jun 11, 2024

• adding fide score and jsd metrics

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• Add function to test for niche similarity by comparing max (99th percentile) counts

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• Fix result dataframe

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• Merge branch 'niche_definitions' of https://github.com/scverse/squidpy into niche_definitions

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• Add scores to compare different niche calculations

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• Update doc string and param names

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Commits on Jun 17, 2024

• Update neighborhood profile, Remove utag import

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• Add utag inner product step

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• Fix output; Remove subsetting, neighborhood options, dimreduction and clustering steps

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• Update utag output

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• Add cellcharter aggregation step

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• Update

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• Fix sparse matrix output

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• Fix neighborhood profile calculation

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• Merge branch 'niche_definitions' of https://github.com/scverse/squidpy into niche_definitions

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Commits on Jul 30, 2024

• Merge branch 'main' into niche_definitions

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• Merge branch 'main' into niche_definitions

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Commits on Aug 26, 2024

• Add consensus function

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Commits on Aug 27, 2024

• Add function to build consensus niche

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• Merge branch 'niche_definitions' of https://github.com/scverse/squidpy into niche_definitions

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• Update init

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• Fix _get_initial_niches

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• Merge branch 'niche_definitions' of https://github.com/scverse/squidpy into niche_definitions

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Commits on Aug 30, 2024

• some type fixes for mypy

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• Update utag

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• Merge branch 'main' into niche_definitions

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Commits on Oct 2, 2024

• Update neighborhood profile based approach

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• Fix

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Commits on Oct 8, 2024

• Update CellCharter approach

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• Remove commented-out code

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• Update init; Fix mypy

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• Merge branch 'main' into niche_definitions

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• Add suggested changes from review

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• Add distance option to neighborhood approach

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• Fix docs; Fix relative frequency calculation; Update arg validation function name

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