Code

Updating v1.1.0 to v1.2.0#194

Code

Merged

ghar1821 merged 84 commits intomasterImmuneDynamics/Spectre:masterfrom v1.2.0-betaImmuneDynamics/Spectre:v1.2.0-betaCopy head branch name to clipboardJul 19, 2024

+3,838-2,973,592

Commits

Commits on Feb 29, 2024

• test ci

  ghar1821

  committed
  b6718f8

• Update check-standard.yaml

  Show description for eab4a1d
  ghar1821

  committed
  eab4a1d

• Update check-standard.yaml

  ghar1821

  authored
  993f7f9

• remove test for now

  ghar1821

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  ff5a8bb

• still errorring god..

  ghar1821

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  68201f3

Commits on May 17, 2024

• Replacing requires

  tomashhurst

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  3e5b5f0

• Update DESCRIPTION and update requires

  tomashhurst

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  a0eed28

• Ad biocViews

  tomashhurst

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• ROxygen2 documentation

  tomashhurst

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  640d767

• Package requirement adjustments

  tomashhurst

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  888aafb

• Checks after new install test

  tomashhurst

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  4699723

• Updated documentation for create.sumtable and prep.cytonorm

  tomashhurst

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  081ed9b

Commits on May 20, 2024

• Update README.md

  tomashhurst

  authored
  fdca270

• Update DESCRIPTION

  tomashhurst

  authored
  cc58f68

• Removing datasets for cleanup

  tomashhurst

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  87426f9

Commits on May 22, 2024

• Updating workflows

  tomashhurst

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  c1c4021

• Updating run.rpca to work with Seurat v5

  tomashhurst

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  91483f2

• Remove import of Seurat and Matrix from run.rpca

  tomashhurst

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  141f1e4

• ROxygen documentation updates

  tomashhurst

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  70dac01

• Update Spectre rPCA.R

  tomashhurst

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  87eb5aa

Commits on May 23, 2024

• Update README.md

  tomashhurst

  authored
  cfc3508

• Update CytoNorm workflow.R

  tomashhurst

  committed
  6fc61b3

• Merge branch 'updates' of https://github.com/ImmuneDynamics/Spectre into updates

  tomashhurst

  committed
  d660ef1

• Update Spectre simple discovery workflow.R

  tomashhurst

  committed
  5b0c2b4

• Update do.add.cols.R

  tomashhurst

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  de3848e

Commits on May 24, 2024

• Merge branch 'updates' into introduce_ci

  ghar1821

  committed
  f7ba966

• Update check-standard.yaml

  ghar1821

  committed
  8aa8085

• Update check-standard.yaml

  ghar1821

  committed
  25eb1ef

• Update check-standard.yaml

  ghar1821

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  2ca8a22

• Update check-standard.yaml

  ghar1821

  committed
  62d0b90

• Update run.pca.R

  ghar1821

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  4f48141

• Update do.add.cols.Rd

  tomashhurst

  committed
  191d0c9

• Updating spatial functions and workflows to remove reliance on rgeos and rgdal and other fixes

  tomashhurst

  committed
  7a5367f

• Further updates to spatial functions and workflows

  tomashhurst

  committed
  42a3e69

• Update README.md

  tomashhurst

  committed
  0802dbc

• Update README.md

  tomashhurst

  authored
  4716238

• Update README.md

  tomashhurst

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  449db5c

• Update README.md

  tomashhurst

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  4cce125

• Update README.md

  tomashhurst

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  1fb5403

• Add directory instructions to spatial workflows

  tomashhurst

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  ea75752

• Merge branch 'updates' of https://github.com/ImmuneDynamics/Spectre into updates

  tomashhurst

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  9fd73b2

• Spatial package updates

  tomashhurst

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  eab108b

• Update Spectre rPCA.R

  tomashhurst

  committed
  57b560b

• Merge pull request #191 from ImmuneDynamics/updates

  Show description for 722ec91
  tomashhurst

  authored
  722ec91

• Update README.md

  tomashhurst

  authored
  25324da

• Update DESCRIPTION

  tomashhurst

  authored
  bd98885

• Update DESCRIPTION

  tomashhurst

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  1275c87

• Update check-standard.yaml

  ghar1821

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• redo docs

  ghar1821

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  da1c026

• Merge remote-tracking branch 'origin/v1.2.0-beta' into introduce_ci

  ghar1821

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  41369c8

• Update check-standard.yaml

  ghar1821

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  700a68e

Commits on May 25, 2024

• Update do.add.cols.R

  ghar1821

  committed
  ddacced

• Update do.add.cols.Rd

  ghar1821

  committed
  3b6ff93

• attempt to fix examples..

  ghar1821

  committed
  c567b87

• Update check-standard.yaml

  ghar1821

  committed
  6cb82a3

• Update check-standard.yaml

  ghar1821

  committed
  e5572ca

Commits on Jun 5, 2024

• Merge pull request #192 from ImmuneDynamics/introduce_ci

  Show description for 336c2ca
  tomashhurst

  authored
  336c2ca

• Update Spectre simple discovery workflow.R

  tomashhurst

  authored
  7483277

• Update CytoNorm workflow.R

  tomashhurst

  authored
  61ab9e8

• Update Spectre rPCA.R

  tomashhurst

  authored
  acef1db

• Update TIFF to FCS.R

  tomashhurst

  authored
  4885a97

• Update Adv spatial 1 - add masks.R

  tomashhurst

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  44b7021

• Update Simple spatial 1 - add masks.R

  tomashhurst

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  291330c

• Update ChronoClust.R

  tomashhurst

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  c5768e8

• Update Segmentation - process TIFFs.R

  tomashhurst

  authored
  94362de

Commits on Jul 8, 2024

• small updates to examples

  ghar1821

  committed
  666b03a

• small updates

  ghar1821

  committed
  0e914ef

Commits on Jul 19, 2024

• Update Spectre rPCA.R

  tomashhurst

  committed
  e07ed6a

• Update run.umap.R

  ghar1821

  committed
  e3519e8

• Merge branch 'v1.2.0-beta' of https://github.com/ImmuneDynamics/Spectre into v1.2.0-beta

  ghar1821

  committed
  14cdb2f

• update doc for umap

  ghar1821

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  69c528a

• run.umap updates to examples

  tomashhurst

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  f911d24

• Update run.rpca.R

  tomashhurst

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  f830b8c

• rpca fixes

  tomashhurst

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  4d4908d

• Update Spectre rPCA.R

  tomashhurst

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  8559472

• add fast plots and removed deprecated functions

  ghar1821

  committed
  a22040b

• Merge branch 'v1.2.0-beta' of https://github.com/ImmuneDynamics/Spectre into v1.2.0-beta

  ghar1821

  committed
  c0bc9bd

• Update fast.colour.plot.R

  ghar1821

  committed
  2c96911

• rPCA updates

  tomashhurst

  committed
  18f9e3f

• Update run.rpca.R

  ghar1821

  committed
  8101872

• Merge branch 'v1.2.0-beta' of https://github.com/ImmuneDynamics/Spectre into v1.2.0-beta

  ghar1821

  committed
  d074316

• Update run.rpca.Rd

  ghar1821

  committed
  6c76a2b

• Update README.md

  tomashhurst

  authored
  2fee898

• Update DESCRIPTION

  tomashhurst

  authored
  6454308