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feat: dbverse integration#213

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Commits on Jan 11, 2024

• Add dbMatrix to colSums_flex and t_flex

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Commits on Jan 12, 2024

• feat: update .evaluate_expr_matrix() and readExprMatrix() for dbMatrix object support

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• feat: update class check to dbSparseMatrix

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• feat: update class check to dbSparseMatrix

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• fix typo in colmeans_flex()

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Commits on Feb 7, 2024

• Merge pull request #163 from drieslab/main

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Commits on Feb 21, 2024

• chore: update .evaluate_expr_matrix gstop message

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• Merge pull request #171 from drieslab/main

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• fix: rowMeans_flex dbMatrix::rowMeans call

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Commits on Mar 23, 2024

• Merge remote-tracking branch 'origin/dev' into db

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• Merge branch 'main' into db

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Commits on Jul 18, 2024

• chore: update dbMatrix constructor name

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Commits on Jul 29, 2024

• Merge remote-tracking branch 'origin/dev' into db

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Commits on Aug 28, 2024

• chore: gitignore pkgdown

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• Add: pip_packages param to allow repository selection when install conda env

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• Merge pull request #228 from wwang-chcn/dev

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Commits on Aug 29, 2024

• Fix functions to be generalizable for more datasets

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Commits on Aug 30, 2024

• fix: dimnames/colnames generics

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• chore: update news

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• Merge branch 'dev' into dev

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• Merge pull request #232 from sjcshin/dev

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• fix: joinGiottoObject

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• Merge branch 'dev' of https://github.com/drieslab/GiottoClass into dev

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• chore: update news

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• chore: bump version for dev

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• chore: add initial join tests

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• Update methods-plot.R

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Commits on Sep 5, 2024

• enh: instructions() updates

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Commits on Sep 9, 2024

• fix: dummy spatlocs prov

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• chore: update join code

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• chore: add missing docs

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• feat!: stop exporting deprecated accessors

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• chore: document

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• chore: update Seurat converter (NNnet) code

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• chore: docs

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Commits on Sep 10, 2024

• fix: update t() for dbMatrix

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• Merge remote-tracking branch 'origin/dev' into db

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• fix: gefToGiotto()

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• fix: prevent unintended init during load

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• feat: accessor check_preqs param

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• feat: initialize param for initialize()

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• feat: bracket and subset() for giotto

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• Merge pull request #234 from jiajic/subset

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Commits on Sep 11, 2024

• fix: expression matrix subsetting error

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• feat: [ and subset() for giotto

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• chore: docs

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• chore: bioc style

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• Update methods-extract.R

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• fix: subset_giotto docs and implementation

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Commits on Sep 12, 2024

• chore: update for [ being internal

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• fix: cast array type to int in gefToGiotto()

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• enh: allow giotto validity skipping using option

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• enh: add dims to print method

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• enh: as.list() for giotto

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• fix: checking option default

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• fix?: try adding S3 as.list() generic

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• Revert "fix?: try adding S3 as.list() generic"

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Commits on Sep 16, 2024

• enh: return NA when unsupported class for nesting generics

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• chore: docs

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• feat!: revert check_preqs in setters

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• enh: sliceGiotto() now sets the active feat/spat

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• enh: add 'giotto.init' option

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• enh: setGiotto() now only inits and checks at once all items in list are added

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• Update NEWS.md

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• enh: [, [[, $ methods

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• chore: docs

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• fix: make dim red getter find defaults

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• enh: spatValues to also check spatlocs and dimreduc

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• chore: docs

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• fix: assertion check

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Commits on Sep 17, 2024

• fix: dbrkt filters need to be vectorized |

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Commits on Sep 18, 2024

• feat: experimental rbind for meta objects

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Commits on Sep 19, 2024

• feat: subset arg for spatIDs() and featIDs()

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• chore: docs

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• chore: news

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• feat: add NSE escape hatch as quote param

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• feat: negate param for interactive subset funs

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Commits on Sep 23, 2024

• Enhance Seurat interoperability for Xenium dataset support

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• Merge pull request #235 from iqraAmin/dev

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• fix: py init

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Commits on Sep 24, 2024

• feat: drop arg for [[ subsetting

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• chore: docs

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• fix: export dollarnames

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• remove calling to inexistent dataset "stxBrain"

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Commits on Sep 25, 2024

• run devtools::document

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• add params description

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• add params description

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• remove duplicated params

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• replace readGiottoInstructions -> instructions

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• add test using RDS method

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• add overwrite = TRUE to solve test error

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• Merge pull request #236 from josschavezf/dev

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• try new workflow

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• Merge branch 'dev' of https://github.com/josschavezf/GiottoClass into dev

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• add packages

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• remove reference to Giottovisuals function to avoid warning in rcmdcheck

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• remove calling for Giotto

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• remove calling to GiottoVisuals

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• add returns value

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• add OS

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• install dev

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• remove calling to Giotto package

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• fix documentation warnings

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• change installation instruction

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• run first bioccheck

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Commits on Sep 26, 2024

• add returns value

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• Merge pull request #237 from josschavezf/dev

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Commits on Sep 27, 2024

• fix: as.list docs

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Commits on Sep 30, 2024

• change rcmdcheck run

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• update R version

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Commits on Oct 1, 2024

• Merge pull request #238 from josschavezf/dev

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Commits on Oct 2, 2024

• Update DESCRIPTION

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• Update DESCRIPTION

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Commits on Oct 3, 2024

• enh: improve objHistory() printing

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• chore: styling

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• change: deprecate and replace showProcessingSteps

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• chore: param doc

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• enh: add param recording escape hatch

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• chore: docs

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Commits on Oct 8, 2024

• enh: $<- for giotto

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• enh: nrow(), ncol(), dim() for giotto

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• enh: ext for affine2d

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Commits on Oct 9, 2024

• enh: dimnames for giotto

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Commits on Oct 10, 2024

• fix: this error message didn't work

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• feat: splitGiotto

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• Update NEWS.md

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Commits on Oct 11, 2024

• chore: remove unneeded code

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• chore: remove unneeded code

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• Update join.R

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• enh: spatValues accesses multiple spat units

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• fix: issue where image features are assumed to be points features

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• Update NEWS.md

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• chore: docs

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Commits on Oct 13, 2024

• chore: remove unnecessary rd

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• chore: docs

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• chore: remove extra import tags

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• chore: further cleanup imports

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• Update NAMESPACE

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• enh: [] for giottoImage and giottoLargeImage

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• enh: as.points for spatLocsObj

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Commits on Oct 15, 2024

• feat: relate, +, -, symdif, intersect, union, snap

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• chore: docs

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• Update spat_binary_ops.Rd

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• !feat: remove combineSpatialCellFeatureInfo()

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• chore: move sp to suggests

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Commits on Oct 17, 2024

• enh: createGiottoLargeImage now works for all things rast does

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• chore: docs

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• fix: createGiottoPolygonsFromMask() shift step functions now actually work as steps

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• chore: update news

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• feat: XY() and XY<-() for coord access

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Commits on Oct 18, 2024

• enh: feat meta + matrix joining can select ids

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Commits on Oct 21, 2024

• fix: ":all:" passing for subsetGiotto

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• fix: poly subsetting now matches spatlocs when possible

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• chore: docs

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• enh: relate method for giotto

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• chore: update relate docs

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Commits on Oct 22, 2024

• feat: doDeferred()

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• Merge pull request #240 from jiajic/defer

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Commits on Oct 23, 2024

• chore: init 3d engine option

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• fix: subsetGiottoLocs() subsets to be inclusive

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Commits on Oct 24, 2024

• Update NEWS.md

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Commits on Oct 25, 2024

• chore: add some comments

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• fix: giottoAffineImage load after save

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• Update NEWS.md

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Commits on Oct 26, 2024

• feat: convHull()

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• chore: deps cleanup

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• chore: docs

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• feat: area()

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• Update NEWS.md

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• fix: prevent terra namespace conflict

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Commits on Oct 27, 2024

• chore: styler

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• chore: docs

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• fix: make sure images are updated after load

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• fix: XY spatlocs method

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• remove extraneous ...

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• change: remove + - in favor of just union and erase

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• chore: deprecated accessor docs cleanup

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• fix: default setting in createNetwork()

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• fix: makePseudoVisium()

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• enh: include_feat_coord for saving

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• temp: drop R version

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• fix: exprmat rowname reading

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• chore: update createGiottoPoints to vmsg

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• Update Seurat and Giotto Interoperability for Xenium Image

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• fix: metadata desync after joining

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• fix: update reconnection for affine images

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• fix: saveGiotto() make image save optional. Also update filepath to saved images

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• enh: list methods for spatUnit and featType

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• Merge branch 'dev' into dev

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• Merge branch 'dev' into db

  

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