Updating v1.1.0 to v1.2.0 #194

tomashhurst · 2024-07-19T06:41:50Z

Major updates to Spectre in v1.2.0. Highlights:

Greatly simplified package dependencies
Reduction in the size of internally stored datasets. Data moved to https://github.com/ImmuneDynamics/data
Fast UMAP implementation (run.umap)
Fast plotting options (fast.colour.plot and fast.multi.plot)
Fast generation of summary statistics (create.sumtable)
Batch integration methods with rPCA (run.rpca)
Minor fixes in CytoNorm and spatial workflows
Inclusion of CI tests

have to switch the push on just to test.

…nto updates

Add CI

… into v1.2.0-beta

ghar1821 and others added 30 commits February 29, 2024 11:08

test ci

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Update check-standard.yaml

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have to switch the push on just to test.

Update check-standard.yaml

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remove test for now

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still errorring god..

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Replacing requires

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Update DESCRIPTION and update requires

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Ad biocViews

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ROxygen2 documentation

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Package requirement adjustments

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Checks after new install test

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Updated documentation for create.sumtable and prep.cytonorm

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Update README.md

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Update DESCRIPTION

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Removing datasets for cleanup

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Updating workflows

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Updating run.rpca to work with Seurat v5

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Remove import of Seurat and Matrix from run.rpca

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ROxygen documentation updates

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Update Spectre rPCA.R

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Update README.md

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Update CytoNorm workflow.R

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Merge branch 'updates' of https://github.com/ImmuneDynamics/Spectre i…

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…nto updates

Update Spectre simple discovery workflow.R

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Update do.add.cols.R

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Merge branch 'updates' into introduce_ci

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Update check-standard.yaml

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Update check-standard.yaml

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Update check-standard.yaml

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Update check-standard.yaml

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tomashhurst and others added 28 commits June 5, 2024 11:00

Merge pull request #192 from ImmuneDynamics/introduce_ci

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Add CI

Update Spectre simple discovery workflow.R

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Update CytoNorm workflow.R

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Update Spectre rPCA.R

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Update TIFF to FCS.R

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Update Adv spatial 1 - add masks.R

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Update Simple spatial 1 - add masks.R

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Update ChronoClust.R

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Update Segmentation - process TIFFs.R

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small updates to examples

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small updates

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Update Spectre rPCA.R

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Update run.umap.R

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

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… into v1.2.0-beta

update doc for umap

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run.umap updates to examples

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Update run.rpca.R

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rpca fixes

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Update Spectre rPCA.R

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add fast plots and removed deprecated functions

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

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… into v1.2.0-beta

Update fast.colour.plot.R

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rPCA updates

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Update run.rpca.R

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

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… into v1.2.0-beta

Update run.rpca.Rd

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Update README.md

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Update DESCRIPTION

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tomashhurst self-assigned this Jul 19, 2024

ghar1821 merged commit ff5314f into master Jul 19, 2024
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Updating v1.1.0 to v1.2.0 #194

Updating v1.1.0 to v1.2.0 #194

tomashhurst commented Jul 19, 2024

Updating v1.1.0 to v1.2.0 #194

Updating v1.1.0 to v1.2.0 #194

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tomashhurst commented Jul 19, 2024