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chore: catch up to suite#1081

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jiajic merged 69 commits intoR4.4.0drieslab/Giotto:R4.4.0from suitedrieslab/Giotto:suiteCopy head branch name to clipboardDec 9, 2024

+6,250-5,054

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Commits on Oct 16, 2024

• temp

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Commits on Oct 30, 2024

• chore: bump version for dev and drop remotes

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• Merge pull request #1062 from jiajic/suite_dev

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Commits on Nov 1, 2024

• Merge branch 'suite' into suite_dev

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Commits on Nov 6, 2024

• Update convenience_xenium.R

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• Revert "temp"

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• Merge branch 'suite_dev' into xen_update

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• Update convenience_xenium.R

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• temporarily lower R ver

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• Update convenience_xenium.R

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• Update convenience_xenium.R

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• Update convenience_xenium.R

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• Update convenience_xenium.R

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Commits on Nov 7, 2024

• fix tif path checking

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• Update convenience_xenium.R

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• fix: allow overwrite passing though ...

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• fix: change when image input type is checked

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• fix: missing comma

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• fix: warning that the "focus" dir does not exist

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• fix: focus img dir assignment

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• Update convenience_xenium.R

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• fix: ignore subdirectories within image focus dir

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• add centroid creation step

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• Update convenience_xenium.R

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• enh: update conv. fun

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• revert default changes

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• update prints and run docs

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• Revert "temporarily lower R ver"

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• Merge pull request #1064 from jiajic/xen_update

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• chore: update news

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Commits on Nov 8, 2024

• chore: update news

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• chore: add back remotes

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• Merge pull request #1065 from jiajic/suite_dev

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• Merge pull request #1066 from drieslab/suite_dev

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Commits on Nov 15, 2024

• fix: account for when no morphology focus imgs found

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• fix: focus path detection when no focus directory but image is present

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• Update convenience_xenium.R

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• fix: list naming indexing

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Commits on Nov 16, 2024

• add biocstyle

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• run devtools::document

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• Merge pull request #1070 from josschavezf/suite_dev

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• add website changes

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• Merge branch 'suite_dev' of https://github.com/josschavezf/Giotto into suite_dev

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• Merge pull request #1071 from josschavezf/suite_dev

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• Merge branch 'suite_dev' into suite

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• Merge pull request #1072 from josschavezf/suite

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• chore: merge conflict

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• Merge pull request #1074 from jiajic/suite_dev

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Commits on Nov 19, 2024

• segmentations

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• Merge pull request #1076 from JunxiangXu/suite_dev

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Commits on Nov 20, 2024

• change scrublet seed setting

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• allow access to transcript datatable

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Commits on Nov 21, 2024

• refactor: var explained

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Commits on Nov 22, 2024

• enh: labelTransfer with integration

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• chore: docs

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Commits on Nov 25, 2024

• chore: fix typo

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• fix param passing

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Commits on Nov 26, 2024

• Update clustering.R

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Commits on Dec 4, 2024

• fix: prevent drop during matrix indexing

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Commits on Dec 8, 2024

• enh: labelTransfer() harmony integration

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Commits on Dec 9, 2024

• enh: labelTransfer() harmony integration

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• chore: reexport dotplot

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• chore: update news

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• chore: docs

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• chore: merge conflict

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• chore: docs

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• Update NEWS.md

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• Merge pull request #1079 from jiajic/suite_dev

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• Merge pull request #1080 from drieslab/suite_dev

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