Version: 0.1.0
Date: 2019-09-17
Text: initial commit

Version: 0.2.0
Date: 2019-11-28
Text: The functions calculateSummary, plotCellCounts, and plotDist have
        been added

Version: 0.3.0
Date: 2021-05-07
Text: Added helper functions for spillover correction

Version: 0.3.0
Date: 2021-05-07
Text: Removed redundant functions

Version: 0.3.1
Date: 2021-05-15
Text: readSCEfromTXT accepts list and path

Version: 0.3.2
Date: 2021-05-16
Text: adjusted plotSpotHeatmap function and unit test

Version: 0.3.3
Date: 2021-05-17
Text: unit tests for binAcrossPixels

Version: 0.3.4
Date: 2021-05-18
Text: added readImagefromTXT function and tests

Version: 0.3.5
Date: 2021-05-20
Text: unit tests and docs for filterPixels

Version: 0.3.6
Date: 2021-06-04
Text: added read_steinbock function, docs and tests

Version: 0.3.7
Date: 2021-06-14
Text: added read_cpout function, docs and tests

Version: 0.3.8
Date: 2021-06-30
Text: Adjusted default parameters for read_steinbock function

Version: 0.3.8
Date: 2021-06-30
Text: Added updated test data

Version: 0.3.9
Date: 2021-07-29
Text: Added buildSpatialGraph function

Version: 0.3.9
Date: 2021-07-29
Text: Added plotSpatial function

Version: 0.3.9
Date: 2021-07-29
Text: Added aggregateNeighbors function

Version: 0.3.10
Date: 2021-08-18
Text: Added countInteractions function

Version: 0.3.10
Date: 2021-08-18
Text: Added testInteractions function

Version: 0.3.11
Date: 2021-08-19
Text: Added flip_x, flip_y argument for plotSpatial function

Version: 0.3.11
Date: 2021-08-19
Text: readSCEfromTXT does not require spot names anymore

Version: 0.3.11
Date: 2021-08-19
Text: knn graph construction can be pruned by distance

Version: 0.3.11
Date: 2021-08-19
Text: added

Version: 0.3.12
Date: 2021-09-01
Text: clean up for Bioconductor submission

Version: 0.99.0
Date: 2021-09-14
Text: Bioconductor submission

Version: 0.99.7
Date: 2021-10-10
Text: Added all unit tests

Version: 0.99.7
Date: 2021-10-10
Text: Fixed read_steinbock x/y axis defaults

Version: 0.99.8
Date: 2021-10-11
Text: Added patch detection method

Version: 0.99.9
Date: 2021-10-22
Text: Removed certain unit tests for 64-bit windows

Version: 1.1.1
Date: 2021-11-16
Text: Bug fix in testInteractions: consider now all possible
        combinations of cell types

Version: 1.1.2
Date: 2021-11-28
Text: Moved all helper functions to single script

Version: 1.1.3
Date: 2021-12-15
Text: Bug fix: divide number of interactions by total number of cells
        for classic and patch interaction counting

Version: 1.1.4
Date: 2021-12-23
Text: Added option to restrict the maximum distance between neighbors
        in delaunay triangulation

Version: 1.1.5
Date: 2022-01-07
Text: More specific access of metal tags

Version: 1.1.6
Date: 2022-01-12
Text: Bug fix: correctly index graphs when reading in steinbock data

Version: 1.1.7
Date: 2022-03-30
Text: readSCEfromTXT: only read in last metal occurrence in .txt file
        name

Version: 1.1.8
Date: 2022-04-03
Text: Adjusted read_cpout function to newest pipeline

Version: 1.1.9
Date: 2022-04-19
Text: Bug fix: patchDetection now works on SpatialExperiment object

Version: 1.1.9
Date: 2022-04-19
Text: Fix for release

Version: 1.3.1
Date: 2022-04-28
Text: Bug fix: avoid using factors in testInteraction function for
        group_by

Version: 1.3.2
Date: 2022-05-30
Text: Bug fix: avoid duplication of metadata entries

Version: 1.3.3
Date: 2022-06-03
Text: Bug fix: specify the number of nodes in patchDetection function

Version: 1.3.4
Date: 2022-06-14
Text: Avoid duplicated columns when generating nodes for plotSpatial

Version: 1.3.5
Date: 2022-06-15
Text: Added three spatial context functions

Version: 1.3.6
Date: 2022-07-28
Text: new function to measure size of patch

Version: 1.3.7
Date: 2022-08-11
Text: new function to measure minimal distances to cells of interest

Version: 1.3.8
Date: 2022-10-13
Text: exclude a single validity check to to class changes in the ggraph
        package

Version: 1.3.9
Date: 2022-10-14
Text: new function for spatial community detection

Version: 1.3.10
Date: 2022-10-22
Text: fix axis.ratio to 1 in plotSpatial function and set scales =
        "fixed"

Version: 1.5.1
Date: 2022-11-22
Text: fix axis.ratio to 1 in plotSpatial function and set scales =
        "fixed"

Version: 1.5.2
Date: 2022-11-23
Text: Bug fix minDistToCells: return NA when all cells of an image
        belong to a patch

Version: 1.5.3
Date: 2023-03-23
Text: Replaced merge function by left_join as safety measure

Version: 1.5.4
Date: 2023-04-04
Text: Added option to get permutation counts returned from
        testInteractions

Version: 1.5.5
Date: 2023-04-20
Text: Bug fix: in corner cases, levels of the permuted factors in the
        testInteractions function do not match the baseline.

Version: 1.5.5
Date: 2023-04-20
Text: Bug fix: testInteractions now works for cells that are not
        ordered by grouping level

Version: 1.5.5
Date: 2023-04-20
Text: Added explicitly message for some functions that the output is
        ordered by image

Version: 1.7.1
Date: 2023-06-07
Text: More info on reproducibility using detectCommunity

Version: 1.7.3
Date: 2023-06-20
Text: More info on reproducibility using testInteractions

Version: 1.7.4
Date: 2023-08-09
Text: Bug fix: correctly setting the "aspect.ratio" argument in
        plotSpatial to fix the physical units of the x- and y-axis

Version: 1.7.5
Date: 2023-09-14
Text: Added more internal validity checks for 'read_steinbock'

Version: 1.7.5
Date: 2023-09-14
Text: Changed the way messages in vroom are silenced

Version: 1.7.5
Date: 2023-09-14
Text: Stop allowing Object numbers to be different between intensities
        and regionprops

Version: 1.7.5
Date: 2023-09-14
Text: Stop allowing missing files in regionprops and neighbors

Version: 1.7.6
Date: 2023-09-26
Text: Updated example data in "inst" to newest version

Version: 1.7.7
Date: 2023-10-02
Text: Bug fix: in rare cases the testInteractions p-values were not
        correctly computed due to machine precision issues

Version: 1.7.8
Date: 2023-10-19
Text: spatialCoords are not initialised with rownames anymore

Version: 1.9.1
Date: 2023-11-20
Text: Switched from aes_ to .data

Version: 1.9.1
Date: 2023-11-20
Text: Initialise SPE and SCE objects with colnames

Version: 1.9.1
Date: 2023-11-20
Text: Additional test within binAcrossPixels

Version: 1.9.2
Date: 2023-12-14
Text: maintainer change

Version: 1.11.1
Date: 2024-10-03
Text: fixed BiocNeighbors error for DFrame type data

Version: 1.11.2
Date: 2024-10-08
Text: fixed testInteraction and countInteraction tests due to machine
        precision issues

Version: 1.11.3
Date: 2024-10-25
Text: fixed testdetectCommunity function

Version: 1.11.4
Date: 2024-10-28
Text: changed testdetectCommunity function for group_by parameter

Version: 1.15.1
Text: Replaced minDistToCells function with distToCells function

Version: 1.15.2
Date: 2025-06-18
Text: Added "interaction" method to countInteractions and
        testInteractions

Version: 1.15.2
Date: 2025-06-18
Text: Added plotInteractions function

Version: 1.15.3
Date: 2025-09-26
Text: Added general zscore output to 'testInteractions()'

Version: 1.15.3
Date: 2025-09-26
Text: Changed name "histocat" method to "conditional" method in
        countInteractions and testInteractions

Version: 1.15.4
Date: 2025-10-08
Text: added readImagefromTIFF function and tests

Version: 1.15.5
Date: 2025-10-20
Text: fixed machine imprecision in tests

Version: 1.15.5
Date: 2025-10-20
Text: fixed test_plotSpatialContext

Version: 1.17.1
Date: 2026-03-30
Text: update function page/vignette

Version: 1.17.2
Date: 2026-04-24
Text: Replaced deprecated aggregateAcrossCells function from scuttle
        package with scrapper implementation

Version: 1.19.1
Date: 2026-05-08
Text: # fixed bug in plotSpotHeatmap function that had also affected
        RELEASE_3_23