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Giotto 4.1.3 #1057
Giotto 4.1.3 #1057
Commits on Aug 13, 2024
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Merge pull request #1011 from jiajic/suite_dev
Suite devfix: allow instructions passing for Xenium conv.
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Commits on Aug 16, 2024
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Merge pull request #1014 from JunxiangXu/suite_dev
loss of igprah call in identifying TMA
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Merge pull request #1015 from josschavezf/suite_dev
update R version
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Commits on Aug 28, 2024
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Commits on Sep 3, 2024
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Merge pull request #1020 from jiajic/suite_dev
chore: move some deps to suggests
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Commits on Sep 4, 2024
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chore: remove deprecated functions & update PAGE example
* remove deprecated `PAGEEnrich()`. Use `runPAGEEnrich()` instead * remove deprecated `rankEnrich()`. Use `runRankEnrich()` instead * remove deprecated `hyperGeometricEnrich()`. Use `runHyperGeometricEnrich()` instead * remove deprecated `createSpatialEnrich()`. Use `runSpatialEnrich()` instead * remove deprecated `heatmSpatialCorGenes()`. Use `heatmSpatialCorFeats()` instead * remove deprecated `runPAGEEnrich_OLD()`. Use `runPAGEEnrich()` instead * update PAGE example * start on reshape2 removal
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Commits on Sep 6, 2024
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Commits on Sep 9, 2024
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Merge pull request #1022 from jiajic/suite_dev
chore: remove some deprecated functions and remove or shift dependencies to modules
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Commits on Sep 13, 2024
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Merge pull request #1023 from jiajic/suite_dev
chore: cleanup some remaining dep accessors
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Commits on Sep 15, 2024
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Commits on Sep 16, 2024
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Merge pull request #1026 from jiajic/suite_dev
chore: refactor pca code
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Commits on Sep 17, 2024
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Merge pull request #1027 from jiajic/suite_dev
chore: refactor pearson norm
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Merge pull request #1028 from jiajic/suite_dev
feat: quantile norm and filter/norm code reorganization
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Commits on Sep 18, 2024
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Merge pull request #1025 from iqraAmin/modular_readers_dev
Update VisiumHD Convenience Function
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Commits on Sep 19, 2024
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Merge pull request #1030 from josschavezf/suite_dev
add function giottoToAnndataZarr
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Commits on Sep 20, 2024
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Commits on Sep 23, 2024
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Merge pull request #1031 from jiajic/suite_dev
feat: labelTransfer & quantile norm
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Commits on Sep 25, 2024
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Merge pull request #1033 from josschavezf/suite_dev
update WNN function to make it more general
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Merge pull request #1037 from josschavezf/suite_dev
update wnn functions
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Merge pull request #1036 from wwang-chcn/suite_dev
Update: integrate with ONTraC
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Merge pull request #1038 from josschavezf/suite_dev
add biocthis style and add missing return values
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update
update_giotto_params()
usage- harmonize param name to `toplevel` - add `toplevel` param where missing - update `toplevel` passing to `update_giotto_params`
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This is now performed in the dim reduction setter
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Merge pull request #1039 from jiajic/suite_dev
feat: NMF implementation and cleanups
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Merge pull request #1040 from jiajic/suite_dev
revert: cluster cells removal. Also some formatting
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Commits on Oct 4, 2024
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fix: upgrade message to error in tsne
- otherwise it will return NULL and wipe the giotto object
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chore: remove jackstraw suggested dep
- for now, we re-implement all needed jackstraw functionalities
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Merge pull request #1042 from jiajic/suite_dev
chore: cleanup jackstraw suggested dep
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- silent return for discovered significant PCs - warning when discovered sig PCs matches ncp
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Merge pull request #1049 from jiajic/suite_dev
!feat: remove re-export of combineSpatialCellFeatureInfo()
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Merge pull request #1052 from jiajic/suite_dev
chore: deprecations for normalizeGiotto
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Commits on Oct 26, 2024
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- has minimal nodes to not be considerd disconnected - now repairs split cores
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enh: update TMA core detection
- change arg repair_split_cores to join_split_cores - add join_tolerance param for area allowed after joining to prevent joins of full cores pairs when the array has very small gutter space.
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