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feat: dbverse integration#213

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Ed2uiz wants to merge 231 commits intomaindrieslab/GiottoClass:mainfrom dbdrieslab/GiottoClass:dbCopy head branch name to clipboard

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Commits on Jan 11, 2024

• Add dbMatrix to colSums_flex and t_flex

  Ed2uiz

  committed
  1de79b0

Commits on Jan 12, 2024

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

  Ed2uiz

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  a8c882d

• feat: update class check to dbSparseMatrix

  Ed2uiz

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  51891eb

• feat: update class check to dbSparseMatrix

  Ed2uiz

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  f960679

• fix typo in colmeans_flex()

  Ed2uiz

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  c7d2341

Commits on Feb 7, 2024

• Merge pull request #163 from drieslab/main

  Show description for ac50c43
  Ed2uiz

  authored
  ac50c43

Commits on Feb 21, 2024

• chore: update .evaluate_expr_matrix gstop message

  Ed2uiz

  committed
  63969fb

• Merge pull request #171 from drieslab/main

  Show description for e3ac636
  Ed2uiz

  authored
  e3ac636

• fix: rowMeans_flex dbMatrix::rowMeans call

  Ed2uiz

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  0eb6d52

Commits on Mar 23, 2024

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

  Ed2uiz

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  cad60db

Commits on Jul 3, 2024

• Merge branch 'main' into db

  Ed2uiz

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  60969cc

Commits on Jul 18, 2024

• chore: update dbMatrix constructor name

  Ed2uiz

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  56a58df

Commits on Jul 29, 2024

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

  Ed2uiz

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  9aab9e2

Commits on Aug 28, 2024

• chore: gitignore pkgdown

  jiajic

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  8638293

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

  wwang-chcn

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  01c6605

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

  Show description for 8c1c4f3
  jiajic

  authored
  8c1c4f3

Commits on Aug 29, 2024

• Fix functions to be generalizable for more datasets

  sjcshin

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  e8858a3

Commits on Aug 30, 2024

• fix: dimnames/colnames generics

  jiajic

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  56f92a1

• chore: update news

  jiajic

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  1e5d90e

• Merge branch 'dev' into dev

  sjcshin

  authored
  93bfde8

• Merge pull request #232 from sjcshin/dev

  Show description for 52b57e0
  jiajic

  authored
  52b57e0

• fix: joinGiottoObject

  Show description for 8fd03d1
  jiajic

  committed
  8fd03d1

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

  jiajic

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  2065f9f

• chore: update news

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  c92a079

• chore: bump version for dev

  jiajic

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  52cf472

• chore: add initial join tests

  jiajic

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  c60c130

• Update methods-plot.R

  jiajic

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  704fe66

Commits on Sep 5, 2024

• enh: instructions() updates

  jiajic

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  103b7e3

Commits on Sep 9, 2024

• fix: dummy spatlocs prov

  jiajic

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  71ba5ce

• chore: update join code

  jiajic

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  ee4abd0

• chore: add missing docs

  jiajic

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  903cc30

• feat!: stop exporting deprecated accessors

  Show description for b4cf4d0
  jiajic

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  b4cf4d0

• chore: document

  Show description for a89a310
  jiajic

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  a89a310

• chore: update Seurat converter (NNnet) code

  Show description for cac3b0e
  jiajic

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  cac3b0e

• chore: docs

  jiajic

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Commits on Sep 10, 2024

• fix: update t() for dbMatrix

  Ed2uiz

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  b7c08bf

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

  Ed2uiz

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  e3cca1c

• fix: gefToGiotto()

  Ed2uiz

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  aba6b3c

• fix: prevent unintended init during load

  jiajic

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  cc12fc6

• feat: accessor check_preqs param

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  jiajic

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  b0da883

• feat: initialize param for initialize()

  Show description for 8063777
  jiajic

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  8063777

• feat: bracket and subset() for giotto

  jiajic

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  d272f5d

• Merge pull request #234 from jiajic/subset

  Show description for 41f11f1
  jiajic

  authored
  41f11f1

Commits on Sep 11, 2024

• fix: expression matrix subsetting error

  jiajic

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  235f5c5

• feat: [ and subset() for giotto

  jiajic

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• chore: docs

  jiajic

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• chore: bioc style

  jiajic

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• Update methods-extract.R

  jiajic

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  e7aaa6b

• fix: subset_giotto docs and implementation

  jiajic

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  acfa06c

Commits on Sep 12, 2024

• chore: update for [ being internal

  jiajic

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  5dc573d

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

  Ed2uiz

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  2872f3a

• enh: allow giotto validity skipping using option

  jiajic

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  461f302

• enh: add dims to print method

  jiajic

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  c597dbc

• enh: as.list() for giotto

  jiajic

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  02797ad

• fix: checking option default

  Show description for 4407875
  jiajic

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  4407875

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

  Show description for 062ab56
  jiajic

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  062ab56

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

  Show description for 360bfe8
  jiajic

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  360bfe8

Commits on Sep 16, 2024

• enh: return NA when unsupported class for nesting generics

  jiajic

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  b4be762

• chore: docs

  jiajic

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  24d08cd

• feat!: revert check_preqs in setters

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  a2079c6

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

  jiajic

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  1529dde

• enh: add 'giotto.init' option

  jiajic

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  1b7b78f

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

  jiajic

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  180383b

• Update NEWS.md

  jiajic

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  abd6f34

• enh: [, [[, $ methods

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  38fd231

• chore: docs

  jiajic

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  cd583f0

• fix: make dim red getter find defaults

  jiajic

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  c1e2539

• enh: spatValues to also check spatlocs and dimreduc

  jiajic

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  7ade099

• chore: docs

  jiajic

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  82c3dc9

• fix: assertion check

  jiajic

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  987ebc8

Commits on Sep 17, 2024

• fix: dbrkt filters need to be vectorized |

  jiajic

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  68a41ba

Commits on Sep 18, 2024

• feat: experimental rbind for meta objects

  jiajic

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Commits on Sep 19, 2024

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

  jiajic

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  dd23e43

• chore: docs

  jiajic

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• chore: news

  jiajic

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• feat: add NSE escape hatch as quote param

  jiajic

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  984db56

• feat: negate param for interactive subset funs

  jiajic

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  5ad0e25

Commits on Sep 23, 2024

• Enhance Seurat interoperability for Xenium dataset support

  iqraAmin

  committed
  91deb23

• Merge pull request #235 from iqraAmin/dev

  Show description for 1e95553
  jiajic

  authored
  1e95553

• fix: py init

  jiajic

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  ddf59a3

Commits on Sep 24, 2024

• feat: drop arg for [[ subsetting

  jiajic

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  5d212dc

• chore: docs

  jiajic

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  6ce7299

• fix: export dollarnames

  jiajic

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  f2f4e09

• remove calling to inexistent dataset "stxBrain"

  josschavezf

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Commits on Sep 25, 2024

• run devtools::document

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• add params description

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  a246648

• add params description

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  e917e56

• remove duplicated params

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  a02130e

• replace readGiottoInstructions -> instructions

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  72027b4

• add test using RDS method

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• add overwrite = TRUE to solve test error

  josschavezf

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• Merge pull request #236 from josschavezf/dev

  Show description for c0cca85
  josschavezf

  authored
  c0cca85

• try new workflow

  josschavezf

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

  josschavezf

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• add packages

  josschavezf

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  7e3c0fa

• remove reference to Giottovisuals function to avoid warning in rcmdcheck

  josschavezf

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  ba03ade

• remove calling for Giotto

  josschavezf

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  0fcfcec

• remove calling to GiottoVisuals

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  f61cbe5

• add returns value

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  5b67180

• add OS

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  ab21cb9

• install dev

  josschavezf

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  a56d602

• remove calling to Giotto package

  josschavezf

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  1872b98

• fix documentation warnings

  josschavezf

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  dca0c4e

• change installation instruction

  josschavezf

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• run first bioccheck

  josschavezf

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  dcc8ec5

Commits on Sep 26, 2024

• add returns value

  josschavezf

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  a348a4a

• Merge pull request #237 from josschavezf/dev

  Show description for cf5558a
  josschavezf

  authored
  cf5558a

Commits on Sep 27, 2024

• fix: as.list docs

  jiajic

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  fa02475

Commits on Sep 30, 2024

• change rcmdcheck run

  josschavezf

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  65d9ab6

• update R version

  josschavezf

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  222eb19

Commits on Oct 1, 2024

• Merge pull request #238 from josschavezf/dev

  Show description for 6ab02d4
  josschavezf

  authored
  6ab02d4

Commits on Oct 2, 2024

• Update DESCRIPTION

  iqraAmin

  authored
  a590339

• Update DESCRIPTION

  iqraAmin

  authored
  d9b5055

Commits on Oct 3, 2024

• enh: improve objHistory() printing

  jiajic

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  70feef1

• chore: styling

  jiajic

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  deaaab4

• change: deprecate and replace showProcessingSteps

  jiajic

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  97431ac

• chore: param doc

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• enh: add param recording escape hatch

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• chore: docs

  jiajic

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  d337512

Commits on Oct 8, 2024

• enh: $<- for giotto

  jiajic

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  ce1e3c0

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

  jiajic

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  7930c7a

• enh: ext for affine2d

  jiajic

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  69d008b

Commits on Oct 9, 2024

• enh: dimnames for giotto

  jiajic

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  161e974

Commits on Oct 10, 2024

• fix: this error message didn't work

  Show description for 9262de3
  jiajic

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  9262de3

• feat: splitGiotto

  jiajic

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  69420a7

• Update NEWS.md

  jiajic

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  d3d06c8

Commits on Oct 11, 2024

• chore: remove unneeded code

  jiajic

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  1ccf2f5

• chore: remove unneeded code

  jiajic

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  01b0a38

• Update join.R

  jiajic

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  afe32e3

• enh: spatValues accesses multiple spat units

  jiajic

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  9c34176

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

  jiajic

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  cf7a633

• Update NEWS.md

  jiajic

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  8bb1e8d

• chore: docs

  jiajic

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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

  jiajic

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  bde44d2

• enh: [] for giottoImage and giottoLargeImage

  jiajic

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  228fbb5

• enh: as.points for spatLocsObj

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Commits on Oct 15, 2024

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

  jiajic

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• chore: docs

  jiajic

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  ba2e552

• Update spat_binary_ops.Rd

  jiajic

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  4e12bc0

• !feat: remove combineSpatialCellFeatureInfo()

  Show description for e0624c2
  jiajic

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  e0624c2

• chore: move sp to suggests

  jiajic

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  1194d1b

Commits on Oct 17, 2024

• enh: createGiottoLargeImage now works for all things rast does

  jiajic

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• chore: docs

  jiajic

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  f216181

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

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• chore: update news

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  7f54f03

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

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Commits on Oct 18, 2024

• enh: feat meta + matrix joining can select ids

  Show description for 549d6e0
  jiajic

  committed
  549d6e0

Commits on Oct 21, 2024

• fix: ":all:" passing for subsetGiotto

  jiajic

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  d6468bb

• fix: poly subsetting now matches spatlocs when possible

  jiajic

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• chore: docs

  jiajic

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• enh: relate method for giotto

  jiajic

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• chore: update relate docs

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Commits on Oct 22, 2024

• feat: doDeferred()

  jiajic

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  8cc4dec

• Merge pull request #240 from jiajic/defer

  Show description for a6d1641
  jiajic

  authored
  a6d1641

• chore: docs

  jiajic

  committed
  d5be937

• chore: docs

  jiajic

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Commits on Oct 23, 2024

• chore: init 3d engine option

  jiajic

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  ead8fae

• fix: subsetGiottoLocs() subsets to be inclusive

  jiajic

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  be5db47

Commits on Oct 24, 2024

• Update NEWS.md

  jiajic

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  ffde2f1

Commits on Oct 25, 2024

• chore: add some comments

  jiajic

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  9df41f6

• fix: giottoAffineImage load after save

  jiajic

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  3ad051a

• Update NEWS.md

  jiajic

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Commits on Oct 26, 2024

• feat: convHull()

  jiajic

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• chore: deps cleanup

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• chore: docs

  jiajic

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• feat: area()

  jiajic

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• Update NEWS.md

  jiajic

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  9bf8d53

• fix: prevent terra namespace conflict

  jiajic

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Commits on Oct 27, 2024

• chore: styler

  jiajic

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• chore: docs

  jiajic

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• fix: make sure images are updated after load

  jiajic

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• fix: XY spatlocs method

  jiajic

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• remove extraneous ...

  jiajic

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  223bf46

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

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  jiajic

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  4696835

• chore: docs update for convHull

  jiajic

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• chore: fix docs

  jiajic

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  114f477

• Update NEWS.md

  jiajic

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• Update DESCRIPTION

  jiajic

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  edd1563

• Merge branch 'main' into dev

  jiajic

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• chore: bump version and remove remotes for dev

  jiajic

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  d15487d

• Revert "chore: bump version and remove remotes for dev"

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  jiajic

  committed
  23a475a

• Reapply "chore: bump version and remove remotes for dev"

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  jiajic

  committed
  a6cf96e

Commits on Oct 28, 2024

• chore: deprecated accessor docs cleanup

  jiajic

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• feat: buffer() and settleGeom

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• Update buffer.R

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• Update NEWS.md

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• chore: return remotes

  jiajic

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• chore: bump version for dev

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  jiajic

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  2571f66

Commits on Oct 29, 2024

• fix: default setting in createNetwork()

  jiajic

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Commits on Oct 30, 2024

• fix: makePseudoVisium()

  jiajic

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• chore: return remotes

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• chore: fix docs

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• chore: update news

  jiajic

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  c246ccb

• chore: bump ver for dev

  Show description for ffb1d94
  jiajic

  committed
  ffb1d94

Commits on Nov 5, 2024

• enh: include_feat_coord for saving

  jiajic

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• chore: update news

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Commits on Nov 6, 2024

• temp: drop R version

  jiajic

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  c6a7f2b

• fix: exprmat rowname reading

  jiajic

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  cbd6470

• fix warning handling

  jiajic

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  38c9c4b

• Revert "temp: drop R version"

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  jiajic

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  4521653

• Update NEWS.md

  jiajic

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  e13901e

• Merge pull request #246 from jiajic/fix_readExprMat

  Show description for 3b344e2
  jiajic

  authored
  3b344e2

Commits on Nov 7, 2024

• chore: update createGiottoPoints to vmsg

  jiajic

  committed
  d6adc1c

Commits on Nov 12, 2024

• Update Seurat and Giotto Interoperability for Xenium Image

  iqraAmin

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  49cd813

• fix: metadata desync after joining

  jiajic

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  618d304

• Update NEWS.md

  jiajic

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• chore: return remotes for push

  jiajic

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  261df0b

• chore: bump version and drop remotes for dev

  jiajic

  committed
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Commits on Nov 13, 2024

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

  iqraAmin

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Commits on Nov 14, 2024

• fix: update reconnection for affine images

  jiajic

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  c9471b8

• fix: list function for images

  jiajic

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  187d218

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

  jiajic

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• Update NEWS.md

  jiajic

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• changes to affine image loading

  jiajic

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  0b325c5

• chore: return remotes for push to main

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• chore: update news

  jiajic

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  f9464a0

• Revert "chore: return remotes for push to main"

  Show description for 86bd01f
  jiajic

  committed
  86bd01f

• Update DESCRIPTION

  iqraAmin

  authored
  110c48b

• Update DESCRIPTION

  iqraAmin

  authored
  39b06c7

Commits on Nov 16, 2024

• run biocstyle

  josschavezf

  committed
  2a83ded

• run devtools::document

  josschavezf

  committed
  cebeeb2

• Merge pull request #254 from josschavezf/dev

  Show description for 4a8654f
  josschavezf

  authored
  4a8654f

Commits on Nov 21, 2024

• Update interoperability.R

  Show description for 2f180f8
  iqraAmin

  authored
  2f180f8

• enh: list methods for spatUnit and featType

  jiajic

  committed
  6316d18

Commits on Nov 22, 2024

• Merge branch 'dev' into dev

  jiajic

  authored
  0c91ef3

• Merge pull request #253 from iqraAmin/dev

  Show description for ce275d3
  jiajic

  authored
  ce275d3

Commits on Nov 24, 2024

• Merge branch 'dev' into db

  

  Ed2uiz

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