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Add function for calculating niches#831

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LLehner wants to merge 87 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

  LLehner

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• Fix pre-commit

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• Fix pre-commit

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• Update __init__.py

  LLehner

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• Merge branch 'main' into niche_definitions

  LLehner

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Commits on May 29, 2024

• Add function

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Commits on Jun 8, 2024

• Update

  LLehner

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  38c67fb

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

  LLehner

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  2eb450c

Commits on Jun 11, 2024

• adding fide score and jsd metrics

  quentinblampey

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  86d5efd

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

  LLehner

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• Fix result dataframe

  LLehner

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

  LLehner

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• Add scores to compare different niche calculations

  LLehner

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• Update doc string and param names

  LLehner

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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

  LLehner

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• Fix pre-commit

  LLehner

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  c6d020b

• Add utag inner product step

  LLehner

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  9fa0157

Commits on Jul 10, 2024

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

  LLehner

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  49b51ca

• Update utag output

  LLehner

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• Add cellcharter aggregation step

  LLehner

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  f797ef9

Commits on Jul 15, 2024

• Update

  LLehner

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  bd16795

Commits on Jul 16, 2024

• Fix sparse matrix output

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• Fix neighborhood profile calculation

  LLehner

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

  LLehner

  committed
  8b22409

Commits on Jul 30, 2024

• Merge branch 'main' into niche_definitions

  timtreis

  authored
  cf5a144

Commits on Aug 21, 2024

• Merge branch 'main' into niche_definitions

  timtreis

  authored
  48ae60b

Commits on Aug 26, 2024

• Add consensus function

  LLehner

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  dcc542d

Commits on Aug 27, 2024

• Add function to build consensus niche

  LLehner

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  2568f7c

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

  LLehner

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  adba136

• Update init

  LLehner

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• Fix _get_initial_niches

  LLehner

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  2b47e81

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

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• Add docstring

  LLehner

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• Update

  LLehner

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

  LLehner

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  699b4f0

Commits on Aug 30, 2024

• some type fixes for mypy

  timtreis

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  f449d88

Commits on Oct 1, 2024

• Update utag

  LLehner

  committed
  dcdd9f6

• Merge branch 'main' into niche_definitions

  LLehner

  authored
  12d918c

Commits on Oct 2, 2024

• Update neighborhood profile based approach

  LLehner

  committed
  6638075

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

  LLehner

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• Update doctstring

  LLehner

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  646dbb0

• Fix

  LLehner

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  939de0b

Commits on Oct 8, 2024

• Update CellCharter approach

  LLehner

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  c9b4dc5

• Remove commented-out code

  LLehner

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• Remove draft validation methods

  LLehner

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• Merge branch 'main' into niche_definitions

  LLehner

  authored
  4c17024

• Update init; Fix mypy

  LLehner

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  a64d0fd

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

  LLehner

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• Fix mypy

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• Fix mypy

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• Fix mypy

  LLehner

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• Fix mypy

  LLehner

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Commits on Oct 9, 2024

• Add comments; Remove draft evaluation function

  LLehner

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  cb4e4d1

• Add tests

  LLehner

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  e0a67f5

• Remove unused imports and print statements

  LLehner

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• Fix tests

  LLehner

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• Fix test

  LLehner

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  3e47df8

Commits on Oct 10, 2024

• Fix test

  LLehner

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• Fix test

  LLehner

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  6185c0e

Commits on Oct 14, 2024

• Merge branch 'main' into niche_definitions

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Commits on Nov 12, 2024

• Merge branch 'main' into niche_definitions

  LLehner

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• Fix sepal

  LLehner

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Commits on Nov 18, 2024

• Merge branch 'main' into niche_definitions

  LLehner

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  37af73d

Commits on Nov 30, 2024

• Add suggested changes from review

  LLehner

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  ca753a2

Commits on Dec 1, 2024

• Add distance option to neighborhood approach

  LLehner

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  e1b2814

Commits on Dec 4, 2024

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

  LLehner

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  91895cd

• Fix tests

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• Fix tests

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Commits on Dec 9, 2024

• Update tests

  LLehner

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• Fix tests

  LLehner

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• Fix tests

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• Fix tests

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• Fix tests

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• Fix tests

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• Merge branch 'main' into niche_definitions

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