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Giotto 4.1.3 #1057

Merged
merged 147 commits into from
Oct 28, 2024
Merged

Giotto 4.1.3 #1057

merged 147 commits into from
Oct 28, 2024

Commits on Aug 13, 2024

  1. fix: allow instructions passing for Xenium conv.

    @jiajic
    jiajic committed Aug 13, 2024
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  2. chore: bump version and update news

    @jiajic
    jiajic committed Aug 13, 2024
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  3. Merge branch 'drieslab:suite_dev' into suite_dev

    @jiajic
    jiajic authored Aug 13, 2024
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  4. Merge pull request #1011 from jiajic/suite_dev 

    Suite devfix: allow instructions passing for Xenium conv.
    @jiajic
    jiajic authored Aug 13, 2024
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Commits on Aug 16, 2024

  1. Update spatial_clusters.R

    @JunxiangXu
    JunxiangXu authored Aug 16, 2024
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  2. Merge pull request #1014 from JunxiangXu/suite_dev 

    loss of igprah call in identifying TMA
    @RubD
    RubD authored Aug 16, 2024
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  3. update R version

    @josschavezf
    josschavezf committed Aug 16, 2024
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  4. Merge pull request #1015 from josschavezf/suite_dev 

    update R version
    @josschavezf
    josschavezf authored Aug 16, 2024
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Commits on Aug 28, 2024

  1. Refine: format, document, and genernalized funcs

    @wwang-chcn
    wwang-chcn committed Aug 28, 2024
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  2. Add: install ontrac env func

    @wwang-chcn
    wwang-chcn committed Aug 28, 2024
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Commits on Sep 3, 2024

  1. chore: move some deps to suggests

    @jiajic
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  2. Merge pull request #1020 from jiajic/suite_dev 

    chore: move some deps to suggests
    @jiajic
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  3. Add: install and run ONTraC through Giotto funcs

    @wwang-chcn
    wwang-chcn committed Sep 3, 2024
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Commits on Sep 4, 2024

  1. chore: update GiottoUtils requirement

    @jiajic
    jiajic committed Sep 4, 2024
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  2. 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
    @jiajic
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  3. chore: reflow example

    @jiajic
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  4. chore: remove progressr. Use giottoutils export

    @jiajic
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  5. chore: fix cellProximityEnrichmentSpots() example

    @jiajic
    jiajic committed Sep 4, 2024
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  6. chore: finish removing reshape2 

    - fix `findICFSpot()` example
    @jiajic
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  7. chore: remove jsonlite references

    @jiajic
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  8. chore: remove packages moved to GiottoUtils

    @jiajic
    jiajic committed Sep 4, 2024
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Commits on Sep 6, 2024

  1. Change: param name, add more descriptions

    @wwang-chcn
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  2. Merge remote-tracking branch 'upstream/suite_dev' into suite_dev

    @wwang-chcn
    wwang-chcn committed Sep 6, 2024
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  3. chore: isolate cowplot dep to GiottoVisuals

    @jiajic
    jiajic committed Sep 6, 2024
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  4. Add: normalization param

    @wwang-chcn
    wwang-chcn committed Sep 6, 2024
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  5. Update: doc

    @wwang-chcn
    wwang-chcn committed Sep 6, 2024
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Commits on Sep 9, 2024

  1. Remove: unused function

    @wwang-chcn
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  2. Update: using shell to run ONTraC

    @wwang-chcn
    wwang-chcn committed Sep 9, 2024
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  3. Update: normalization param

    @wwang-chcn
    wwang-chcn committed Sep 9, 2024
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Commits on Sep 11, 2024

  1. change: deprecate name arg in screePlot()

    @jiajic
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Commits on Sep 12, 2024

  1. chore: remove some deps and some deprecated functions

    @jiajic
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  2. chore: bump version for dev

    @jiajic
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  3. chore: update deprecated accessors

    @jiajic
    jiajic committed Sep 12, 2024
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  4. Merge pull request #1022 from jiajic/suite_dev 

    chore: remove some deprecated functions and remove or shift dependencies to modules
    @jiajic
    jiajic authored Sep 12, 2024
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Commits on Sep 13, 2024

  1. chore: cleanup some remaining dep accessors

    @jiajic
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  2. Merge pull request #1023 from jiajic/suite_dev 

    chore: cleanup some remaining dep accessors
    @jiajic
    jiajic authored Sep 13, 2024
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Commits on Sep 15, 2024

  1. Update VisiumHD Convenience Function

    @iqraAmin
    iqraAmin committed Sep 15, 2024
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Commits on Sep 16, 2024

  1. chore: refactor pca code

    @jiajic
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  2. Merge pull request #1026 from jiajic/suite_dev 

    chore: refactor pca code
    @jiajic
    jiajic authored Sep 16, 2024
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Commits on Sep 17, 2024

  1. chore: minor edits

    @jiajic
    jiajic committed Sep 17, 2024
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  2. chore: minor edits

    @jiajic
    jiajic committed Sep 17, 2024
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  3. chore: refactor pearson norm

    @jiajic
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  4. Merge pull request #1027 from jiajic/suite_dev 

    chore: refactor pearson norm
    @jiajic
    jiajic authored Sep 17, 2024
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  5. feat: quantile norm

    @jiajic
    jiajic committed Sep 17, 2024
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  6. chore: fix tags

    @jiajic
    jiajic committed Sep 17, 2024
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  7. chore: code reorganization

    @jiajic
    jiajic committed Sep 17, 2024
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  8. chore: docs

    @jiajic
    jiajic committed Sep 17, 2024
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  9. chore: styler

    @jiajic
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  10. chore: docs

    @jiajic
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  11. Merge pull request #1028 from jiajic/suite_dev 

    feat: quantile norm and filter/norm code reorganization
    @jiajic
    jiajic authored Sep 17, 2024
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Commits on Sep 18, 2024

  1. Update .visiumHD_poly Function

    @iqraAmin
    iqraAmin committed Sep 18, 2024
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  2. Merge pull request #1025 from iqraAmin/modular_readers_dev 

    Update VisiumHD Convenience Function
    @jiajic
    jiajic authored Sep 18, 2024
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Commits on Sep 19, 2024

  1. Init:

    @wwang-chcn
    wwang-chcn committed Sep 19, 2024
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  2. Merge remote-tracking branch 'upstream/suite_dev' into suite_dev

    @wwang-chcn
    wwang-chcn committed Sep 19, 2024
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  3. chore: move ggraph from Suggests to Imports

    @wwang-chcn
    wwang-chcn committed Sep 19, 2024
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  4. chore: fix ONTraC executable path on Windows system

    @wwang-chcn
    wwang-chcn committed Sep 19, 2024
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  5. Remove: unused function

    @wwang-chcn
    wwang-chcn committed Sep 19, 2024
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  6. add function giottoToAnndataZarr

    @josschavezf
    josschavezf committed Sep 19, 2024
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  7. Merge pull request #1030 from josschavezf/suite_dev 

    add function giottoToAnndataZarr
    @josschavezf
    josschavezf authored Sep 19, 2024
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Commits on Sep 20, 2024

  1. Remove: unused param doc

    @wwang-chcn
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  2. Merge remote-tracking branch 'upstream/suite_dev' into suite_dev

    @wwang-chcn
    wwang-chcn committed Sep 20, 2024
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  3. Fix: typo

    @wwang-chcn
    wwang-chcn committed Sep 20, 2024
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  4. Update: docs

    @wwang-chcn
    wwang-chcn committed Sep 20, 2024
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  5. Fix: typo

    @wwang-chcn
    wwang-chcn committed Sep 20, 2024
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  6. chore: remove deprecated harmony functionalities

    @jiajic
    jiajic committed Sep 20, 2024
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  7. feat: labelTransfer()

    @jiajic
    jiajic committed Sep 20, 2024
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  8. chore: docs

    @jiajic
    jiajic committed Sep 20, 2024
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  9. chore: news

    @jiajic
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Commits on Sep 23, 2024

  1. Merge pull request #1031 from jiajic/suite_dev 

    feat: labelTransfer & quantile norm
    @jiajic
    jiajic authored Sep 23, 2024
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Commits on Sep 25, 2024

  1. Update: doc

    @wwang-chcn
    wwang-chcn committed Sep 25, 2024
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  2. Update: ontrac results dirs

    @wwang-chcn
    wwang-chcn committed Sep 25, 2024
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  3. Merge remote-tracking branch 'upstream/suite_dev' into suite_dev

    @wwang-chcn
    wwang-chcn committed Sep 25, 2024
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Commits on Sep 26, 2024

  1. Update: handling niche cluster order

    @wwang-chcn
    wwang-chcn committed Sep 26, 2024
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Commits on Sep 27, 2024

  1. fix typo

    @josschavezf
    josschavezf committed Sep 27, 2024
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  2. fix typo

    @josschavezf
    josschavezf committed Sep 27, 2024
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  3. update wnn function

    @josschavezf
    josschavezf committed Sep 27, 2024
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  4. Merge branch 'drieslab:suite_dev' into suite_dev

    @josschavezf
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  5. Merge pull request #1033 from josschavezf/suite_dev 

    update WNN function to make it more general
    @josschavezf
    josschavezf authored Sep 27, 2024
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  6. update news

    @josschavezf
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  7. Merge pull request #1034 from josschavezf/suite_dev 

    update news
    @josschavezf
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  8. Merge remote-tracking branch 'upstream/suite_dev' into suite_dev

    @wwang-chcn
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Commits on Sep 30, 2024

  1. update wnn functions

    @josschavezf
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  2. Merge branch 'suite_dev' of https://github.com/josschavezf/Giotto int… 

    …o suite_dev
    @josschavezf
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  3. Merge pull request #1037 from josschavezf/suite_dev 

    update wnn functions
    @josschavezf
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Commits on Oct 2, 2024

  1. Merge pull request #1036 from wwang-chcn/suite_dev 

    Update: integrate with ONTraC
    @josschavezf
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  2. run devtools::document

    @josschavezf
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  3. fix typo

    @josschavezf
    josschavezf committed Oct 2, 2024
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  4. run biocthis style

    @josschavezf
    josschavezf committed Oct 2, 2024
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  5. update R version

    @josschavezf
    josschavezf committed Oct 2, 2024
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  6. use biocstyle

    @josschavezf
    josschavezf committed Oct 2, 2024
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  7. remove lazydata

    @josschavezf
    josschavezf committed Oct 2, 2024
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  8. adjust line length

    @josschavezf
    josschavezf committed Oct 2, 2024
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  9. add return values

    @josschavezf
    josschavezf committed Oct 2, 2024
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  10. Merge pull request #1038 from josschavezf/suite_dev 

    add biocthis style and add missing return values
    @josschavezf
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Commits on Oct 3, 2024

  1. fix: allow processGiotto to skip adjust by default

    @jiajic
    jiajic committed Oct 3, 2024
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  2. update update_giotto_params() usage 

    - harmonize param name to `toplevel`
- add `toplevel` param where missing
- update `toplevel` passing to `update_giotto_params`
    @jiajic
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  3. missed some

    @jiajic
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  4. chore: remove name checking 

    This is now performed in the dim reduction setter
    @jiajic
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  5. feat: NMF implementation via RcppML

    @jiajic
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  6. chore: formatting

    @jiajic
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  7. feat: reduceDims() API

    @jiajic
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  8. feat: NMF implementation and cleanups

    @jiajic
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  9. chore: document

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  10. Merge pull request #1039 from jiajic/suite_dev 

    feat: NMF implementation and cleanups
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  11. revert: cluster cells removal. Also some formatting

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  12. chore: docs

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  13. Merge pull request #1040 from jiajic/suite_dev 

    revert: cluster cells removal. Also some formatting
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    jiajic authored Oct 3, 2024
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Commits on Oct 4, 2024

  1. fix: upgrade message to error in tsne 

    - otherwise it will return NULL and wipe the giotto object
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    jiajic committed Oct 4, 2024
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Commits on Oct 7, 2024

  1. update jackstraw permPA

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  2. chore: docs

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    jiajic committed Oct 7, 2024
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  3. Merge branch 'suite_dev' of https://github.com/jiajic/Giotto into sui… 

    …te_dev
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  4. Merge pull request #1041 from jiajic/jstraw 

    change: jackstraw update
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    jiajic authored Oct 7, 2024
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  5. Merge branch 'drieslab:suite_dev' into suite_dev

    @jiajic
    jiajic authored Oct 7, 2024
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  6. chore: remove jackstraw suggested dep 

    - for now, we re-implement all needed jackstraw functionalities
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  7. Merge pull request #1042 from jiajic/suite_dev 

    chore: cleanup jackstraw suggested dep
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    jiajic authored Oct 7, 2024
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  8. Update NEWS.md

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  9. Merge pull request #1043 from jiajic/suite_dev 

    Update NEWS.md
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    jiajic authored Oct 7, 2024
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  10. updates for jackstraw 

    - silent return for discovered significant PCs
- warning when discovered sig PCs matches ncp
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  11. Merge pull request #1044 from jiajic/suite_dev 

    updates for jackstraw
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    jiajic authored Oct 7, 2024
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Commits on Oct 8, 2024

  1. fix: seed setting

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  2. Merge pull request #1045 from jiajic/suite_dev 

    fix: seed setting
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    jiajic authored Oct 8, 2024
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  3. fix warning

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    jiajic committed Oct 8, 2024
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  4. Merge pull request #1046 from jiajic/suite_dev 

    fix warning
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    jiajic authored Oct 8, 2024
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Commits on Oct 12, 2024

  1. chore: formatting

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Commits on Oct 15, 2024

  1. !feat: remove re-export of combineSpatialCellFeatureInfo()

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  2. Merge pull request #1049 from jiajic/suite_dev 

    !feat: remove re-export of combineSpatialCellFeatureInfo()
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    jiajic authored Oct 15, 2024
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  3. fix: doKmeans

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    jiajic committed Oct 15, 2024
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  4. Merge pull request #1050 from jiajic/suite_dev 

    fix: doKmeans
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    jiajic authored Oct 15, 2024
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  5. fix: doHclust()

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    jiajic committed Oct 15, 2024
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  6. Merge pull request #1051 from jiajic/suite_dev 

    fix: `doHclust()`
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    jiajic authored Oct 15, 2024
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  7. chore: deprecations for normalizeGiotto

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    jiajic committed Oct 15, 2024
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Commits on Oct 16, 2024

  1. chore: change libsize 0 detection

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    jiajic committed Oct 16, 2024
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Commits on Oct 17, 2024

  1. Merge pull request #1052 from jiajic/suite_dev 

    chore: deprecations for normalizeGiotto
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    jiajic authored Oct 17, 2024
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Commits on Oct 21, 2024

  1. change: rework spatial splitting to return numeric

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    jiajic committed Oct 21, 2024
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Commits on Oct 26, 2024

  1. enh: identifyTMAcores 

    - has minimal nodes to not be considerd disconnected
- now repairs split cores
    @jiajic
    jiajic committed Oct 26, 2024
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  2. enh: expose angles to test param

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    jiajic committed Oct 26, 2024
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  3. 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.
    @jiajic
    jiajic committed Oct 26, 2024
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Commits on Oct 27, 2024

  1. chore: use new gwith_seed()

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    jiajic committed Oct 27, 2024
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  2. chore: deps cleanups

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    jiajic committed Oct 27, 2024
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  3. Update .Rbuildignore

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    jiajic committed Oct 27, 2024
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Commits on Oct 28, 2024

  1. Update NEWS.md

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    jiajic committed Oct 28, 2024
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  2. Update NEWS.md

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    jiajic committed Oct 28, 2024
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  3. Merge pull request #1055 from jiajic/suite_dev 

    Suite dev
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    jiajic authored Oct 28, 2024
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  4. Update NEWS.md

    @jiajic
    jiajic committed Oct 28, 2024
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  5. Merge pull request #1056 from jiajic/suite_dev 

    update news
    @jiajic
    jiajic authored Oct 28, 2024
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  6. chore: return remotes

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    jiajic committed Oct 28, 2024
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  7. Merge pull request #1058 from jiajic/suite_dev 

    chore: return remotes
    @jiajic
    jiajic authored Oct 28, 2024
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