feat: Ultra-large matrix support and Read10X performance optimization#10017

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BenjaminDEMAILLE:feature/spam-matrix-support

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Commits on Feb 4, 2025

Merge pull request #9666 from satijalab/ci-cleanup
dcollins15
authored

Commits on Feb 5, 2025

Add issue template with helpful hints

rharao
authored and
David Collins
committed
Rename issue template for better ordering in chooser

rharao
authored and
David Collins
committed
Encourage users to ask questions on the discussion board

rharao
authored and
David Collins
committed
Kebab case for consistency

rharao
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David Collins
committed
Kebab case for consistency

rharao
authored and
David Collins
committed
Add ISSUE_TEMPLATE config

rharao
authored and
David Collins
committed
Drop ISSUE_TEMPLATE/documentation.md
David Collins
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Drop ISSUE_TEMPLATE/feature-request.md
David Collins
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Drop ISSUE_TEMPLATE/bug-report.md
David Collins
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Drop ISSUE_TEMPLATE/bug-report-guidied.md
David Collins
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Enable blank issues
David Collins
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Refine analysis-question
David Collins
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Add ISSUE_TEMPLATE/documentation.yml
David Collins
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Add ISSUE_TEMPLATE/feature-request.yml
David Collins
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Add bug-report.yml
David Collins
committed

Commits on Feb 6, 2025

Merge pull request #9671 from satijalab/issue-template-revamp
dcollins15
authored

Commits on Feb 7, 2025

Changing subset technique to work for Seurat V5 for GroupCorrelation() as discussed in issue #9483

joesphbeller
authored and
dcollins15
committed
Changing subset technique to work for Seurat V5 for GroupCorrelationPlot() as discussed in issue #9483

joesphbeller
authored and
dcollins15
committed
Update R/utilities.R

joesphbeller
and
dcollins15
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Implementing @dcollins15 suggestion

joesphbeller
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dcollins15
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Update changelog
David Collins
committed
Bump version
David Collins
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Merge pull request #9625 from joesphbeller/master
dcollins15
authored

Commits on Feb 14, 2025

Fix PercentageFeatureSet to respect assay param

mccormickceci
authored and
David Collins
committed
Tweak feature/pattern warning in PercentageFeatureSet
David Collins
committed

Commits on Feb 25, 2025

Update changelog
David Collins
committed
Bump version
David Collins
committed
Merge pull request #9686 from satijalab/fix/percentage-feature-set
dcollins15
authored
Set default vals for scalefactors to 1
David Collins
committed
Add ScaleFactors.SlideSeq
David Collins
committed
Add ScaleFactors.STARmap
David Collins
committed
Update docs
David Collins
committed
Bump version
David Collins
committed
Update changelog
David Collins
committed

Commits on Feb 26, 2025

Merge pull request #9691 from satijalab/fix/spatialdimplot
dcollins15
authored

Commits on Mar 17, 2025

add raster.dpi for vlnplot

samuel-marsh
authored and
David Collins
committed
add exiplot params

samuel-marsh
authored and
David Collins
committed
roxygenizae to pass checks

samuel-marsh
authored and
David Collins
committed

Commits on Mar 28, 2025

Bump version
David Collins
committed
Update changelog
David Collins
committed
Merge pull request #9665 from samuel-marsh/raster.dpi_vlnplot
dcollins15
authored

Commits on Mar 31, 2025

Drop tests/testthat/test_read_mtx.R
David Collins
committed
Bump version
David Collins
committed
Merge pull request #9790 from satijalab/fix/drop-flaky-tests
dcollins15
authored
HarmonyMatrix to RunHarmony, commented out some deprec args

sarkars
authored and
dcollins15
committed
added warning about unused/deprecated params

sarkars
authored and
dcollins15
committed
deleted the unnecessary comments

sarkars
authored and
dcollins15
committed
edited warning message about dropping parameters

sarkars
authored and
dcollins15
committed
edit to warning message about ignoring params

sarkars
authored and
dcollins15
committed
changed warning function for ignoring params

sarkars
authored and
dcollins15
committed
Passed optional params to harmony options, changed warnings, changed epsilon.harmony to 0.01

sarkars
authored and
dcollins15
committed
roxygenize

David Collins
authored and
dcollins15
committed
Bump version
David Collins
committed
Update changelog
David Collins
committed

Commits on Apr 7, 2025

Merge pull request #9789 from satijalab/fix/harmony-integration
dcollins15
authored

Commits on Apr 17, 2025

Delete no-response.yml
David Collins
committed
Rename integration_checks.yaml -> merge_checks.yaml
David Collins
committed
Update triggers for pre-merge checks
David Collins
committed
Add release_checks.yaml
David Collins
committed
Add reverse_dependency_checks.yaml
David Collins
committed
Update pull_request_template.md
David Collins
committed
Merge pull request #9822 from satijalab/expanded-ci
dcollins15
authored

Commits on Apr 20, 2025

Add RunICA.StdAssay
David Collins
committed
Refactor test_dimensional_reduction.R
David Collins
committed
Add test for RunICA
David Collins
committed
Extend test for RunICA to check BPCells inputs
David Collins
committed
roxygenize
David Collins
committed
Bump version
David Collins
committed
Update changelog
David Collins
committed
Merge pull request #9825 from satijalab/feat/run-ica-std-assay
dcollins15
authored
Fixup test_utilities.R
David Collins
committed
Enabled support for multi-assay

rsatija
authored and
David Collins
committed
Drop .IsFutureSeurat import from PseudobulkExpression
David Collins
committed
roxygenize
David Collins
committed
Bump version
David Collins
committed
Update changelog
David Collins
committed
Merge pull request #9824 from satijalab/fix/pseudobulk-multi-assay
dcollins15
authored
Setting up generic for AddModuleScore

Izzy Grabski
authored and
David Collins
committed
Separated AddModuleScore into AddModuleScore.Seurat and AddModuleScore.Assay

Izzy Grabski
authored and
David Collins
committed
Fixed generic set-up

Izzy Grabski
authored and
David Collins
committed
Added AddModuleScore.StdAssay

Izzy Grabski
authored and
David Collins
committed
Added a test

Izzy Grabski
authored and
David Collins
committed
Tidy docstrings for AddModuleScore
David Collins
committed
roxygenize
David Collins
committed
Bump version
David Collins
committed
Update changelog
David Collins
committed
Merge pull request #9826 from satijalab/feat/module-score-std-assay
dcollins15
authored
Update merge.SCTAssay to use FetchResiduals
David Collins
committed
Rename FetchResiduals -> FetchResiduals.Seurat
David Collins
committed
Add FetchResiduals generic
David Collins
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Add FetchResiduals.SCTAssay
David Collins
committed
Refactor FetchResidualSCTModel for assays
David Collins
committed
Simplify FetchResiduals.Seurat
David Collins
committed
Update FetchResidualSCTModel call in GetResidual
David Collins
committed
Add fill.missing.residuals param to merge.SCTAssay
David Collins
committed
Reimplement SCTransform.StdAssay
David Collins
committed
Revert "Add fill.missing.residuals param to merge.SCTAssay"
David Collins
committed
Add FetchResiduals call to SCTransform.StdAssay
David Collins
committed
Fixup return statements for FetchResiduals.SCTAssay
David Collins
committed
Fixup return types FetchResiduals.Seurat
David Collins
committed
Fixup merge.SCTAssay
David Collins
committed
Loosen tolerance on SketchData tests
David Collins
committed
Fill in missing residuals and compute variable features

Izzy Grabski
authored and
David Collins
committed
Add test for SCTransform v3 v5 consistency

Izzy Grabski
authored and
David Collins
committed
Pass variable.features.n to VariableFeatures

Izzy Grabski
authored and
David Collins
committed
Fixup docstring for FetchResiduals generic
David Collins
committed
Fixup docs & comments for FetchResiduals methods
David Collins
committed
roxygenize
David Collins
committed
Bump version
David Collins
committed
Update changelog
David Collins
committed
Merge pull request #9828 from satijalab/fix/sctransform-stdassay
dcollins15
authored

Commits on Apr 21, 2025

Fix Cells.SCTAssay
David Collins
committed
Drop VariableFeatures call from SketchData
David Collins
committed
Add test case for SketchData and SCTransform
David Collins
committed
Bump version
David Collins
committed
Update changelog
David Collins
committed
Merge pull request #9830 from satijalab/fix/sketch-sct
dcollins15
authored
convert to sparse

yuhanH
authored and
David Collins
committed
Bump version
David Collins
committed
Update changelog
David Collins
committed
Merge pull request #9831 from satijalab/fix/leverage-score-bpcells
dcollins15
authored

Commits on Apr 22, 2025

enable multilayer query when mappingk set

adyzh
authored and
David Collins
committed
findtransferanchors work with mappingk set

adyzh
authored and
David Collins
committed
enable mapscore() layers - debugging

adyzh
authored and
David Collins
committed
Fixing mappingscore()

adyzh
authored and
David Collins
committed
fixing mappingscore(): query anchors subset

adyzh
authored and
David Collins
committed
fixing mappingscore(), map indices to layer-specific positions

adyzh
authored and
David Collins
committed
fixing anchors

adyzh
authored and
David Collins
committed
enabled MappingScore() compatibility with multi-layered queries

adyzh
authored and
David Collins
committed
nit

authored and
David Collins
committed
nit

authored and
David Collins
committed
nit

authored and
David Collins
committed
incorporated code review comments

adyzh
authored and
David Collins
committed
flattened mapping_scores_List

adyzh
authored and
David Collins
committed
refactored mapping_scores_list loop using lappy

adyzh
authored and
David Collins
committed
nitt

adyzh
authored and
David Collins
committed
fixed neighbors list per code review

adyzh
authored and
David Collins
committed
return mapping scores list

adyzh
authored and
David Collins
committed
adding tests for multilayer query, debugging

adyzh
authored and
David Collins
committed
adding tests for MappingScore

adyzh
authored and
David Collins
committed
added findtransferanchors tests for split query

adyzh
authored and
David Collins
committed
fixed mappingscore to enable no precomputed neighbors

adyzh
authored and
David Collins
committed
adding tests for mappingscore()

adyzh
authored and
David Collins
committed
Fixup MappingScore.AnchorSet
David Collins
committed
Tidy tests
David Collins
committed
Revert unnecessary parameter formatting
David Collins
committed
Bump version
David Collins
committed
Update changelog
David Collins
committed
Merge pull request #9832 from satijalab/fix/transfer-multi-query
dcollins15
authored
Fixup docstring for AddModuleScore.Assay
David Collins
committed
Use reference doi in LeverageScore generic
David Collins
committed
Use reference doi in CountSketch
David Collins
committed
roxygenize
David Collins
committed
Bump version
David Collins
committed
Merge pull request #9833 from satijalab/fix/cran-notes
dcollins15
authored
enable findtransferanchors compatibility with integratelayers ref

adyzh
authored and
David Collins
committed
select one sct model for findtransferanchors

adyzh
authored and
David Collins
committed
FindTransferAnchors selects one sct model from integrated reference

adyzh
authored and
David Collins
committed
nit

adyzh
authored and
David Collins
committed
missing function name

adyzh
authored and
David Collins
committed
added conditional check for selecting a single sct model from integrated ref, updated validateparams to check for mixing sct and rna assays

adyzh
authored and
David Collins
committed
Bump version
David Collins
committed
Update changelog
David Collins
committed
Merge pull request #9834 from satijalab/fix/transfer-multi-sct-ref
dcollins15
authored

Commits on Apr 23, 2025

chore: update preprocessing.R

eltociear
authored and
David Collins
committed
Update visualization.R

Liripo
authored and
David Collins
committed
Fix comparison typo in cell retention condition

pormr
authored and
David Collins
committed
Bump version
David Collins
committed
Merge pull request #9835 from satijalab/fix/misc
dcollins15
authored
FindSpatiallyVariableFeatures.StdAssay calls Assay method
David Collins
committed
Deprecate slot with layer in FindSpatiallyVariableFeatures.Assay
David Collins
committed
Deprecate slot with layer in FIndSpatiallyVariableFeatures.Seurat
David Collins
committed
Fix LogSeuratCommand error caused by deprecated default
David Collins
committed
roxygenize
David Collins
committed
Bump version
David Collins
committed
Update changelog
David Collins
committed
Merge pull request #9836 from satijalab/fix/find-svf
dcollins15
authored
change separator from underscore to tilde for ImagePlot functions

zskylarli
authored and
David Collins
committed
Replace tilde with unit separator in ImageDimPlot
David Collins
committed
Replace tilde with unit separator in ImageFeaturePlot
David Collins
committed
Merge pull request #9837 from satijalab/fix/imageplot
dcollins15
authored
Revert "Fix ImageDimPlot & ImageFeaturePlot to allow "_" in FOV names"
dcollins15
authored
Merge pull request #9838 from satijalab/revert-9837-fix/imageplot
dcollins15
authored
Fixup test for MappingScore
David Collins
committed
Bump version
David Collins
committed
Merge pull request #9839 from satijalab/fix/mapping-score-test
dcollins15
authored
minor fix to pass scale.factor and margin arguments

mhkowalski
authored and
David Collins
committed
add AggregateExpression tests

mhkowalski
authored and
David Collins
committed
roxygenize
David Collins
committed
Bump version
David Collins
committed
Update changelog
David Collins
committed
Merge pull request #9840 from satijalab/fix/pseudobulk_params
dcollins15
authored
Fix VariableFeatures.SCTAssay
David Collins
committed
Fix FindVariableFeatures.SCTAssay
David Collins
committed
Rewrite docstring for SCTransform.default
David Collins
committed
roxygenize
David Collins
committed
Bump version
David Collins
committed
Merge pull request #9842 from satijalab/fix/sct-misc
dcollins15
authored
Drop flaky test from test_sketching.R
David Collins
committed
Bump version
David Collins
committed
Merge pull request #9843 from satijalab/fix/test-sketch
dcollins15
authored
Rename stable release branches from release/* to *-stable
David Collins
committed
Merge pull request #9844 from satijalab/update-release-checks-branch
dcollins15
authored
Bump version
David Collins
committed
Update changelog
David Collins
committed
Clear CRAN comments
David Collins
committed
Update stable branch name in merge_checks.yaml
David Collins
committed
Merge pull request #9846 from satijalab/post-release-updates
dcollins15
authored

Commits on May 20, 2025

Add arguments to kmeans call in BuildNicheAssay function
vdsukhov
committed

Commits on May 21, 2025

fix bugs introduced to FindTransferAnchors from 6b1fc3e
zskylarli
committed

Commits on May 27, 2025

Add fallback for variable features from data layer to count layer
YoukaiFromAccounting
committed

Commits on Jun 2, 2025

Fix deprecation errors in NormalizeData for V3 object
YoukaiFromAccounting
committed

Commits on Jun 3, 2025

Merge remote-tracking branch 'seurat-private/fix-leveragescore-and-deprecation' into fix/v5.3.99.9001
zskylarli
committed

Commits on Jun 5, 2025

Commits on Jun 6, 2025

Commits on Jun 10, 2025

Merge pull request #9924 from satijalab/fix/v5.3.1
rsatija
authored

Commits on Jun 13, 2025

Commits on Jun 17, 2025

Refactor: wrap arguments in ellipsis (...) in BuildNicheAssay function
vdsukhov
committed

Commits on Jun 20, 2025

Merge branch 'main' into extra-arguments-for-build-niche-assay
zskylarli
authored

Commits on Jul 25, 2025