Files in BodenmillerGroup/imcRtools
Methods for imaging mass cytometry data analysis
.github/.gitignore
.github/workflows/build-checks-devel.yml
.github/workflows/build-checks-release.yml
.github/workflows/docs.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/aggregateNeighbors.R
R/binAcrossPixels.R
R/buildSpatialGraph.R
R/countInteractions.R
R/detectCommunity.R
R/detectSpatialContext.R
R/filterPixels.R
R/filterSpatialContext.R
R/findBorderCells.R
R/minDistToCells.R
R/patchDetection.R
R/patchSize.R
R/plotSpatial.R
R/plotSpatialContext.R
R/plotSpotHeatmap.R
R/readImagefromTXT.R
R/readSCEfromTXT.R
R/read_cpout.R
R/read_steinbock.R
R/show_cpout_features.R
R/testInteractions.R
R/utils.R
R/validityChecks.R
README.md
inst/CITATION
inst/extdata/mockData/cpout/Experiment.csv
inst/extdata/mockData/cpout/Image.csv
inst/extdata/mockData/cpout/Object_relationships.csv
inst/extdata/mockData/cpout/cell.csv
inst/extdata/mockData/cpout/panel.csv
inst/extdata/mockData/cpout/var_Image.csv
inst/extdata/mockData/cpout/var_cell.csv
inst/extdata/mockData/raw/20210305_NE_mockData2_ROI_001_1.txt
inst/extdata/mockData/raw/20210305_NE_mockData2_ROI_002_2.txt
inst/extdata/mockData/raw/20210305_NE_mockData2_ROI_003_3.txt
inst/extdata/mockData/steinbock/images.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData1_001.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData1_002.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData1_003.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData2_001.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData2_002.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData2_003.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData3_001.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData3_002.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData3_003.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData4_001.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData4_002.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData4_003.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData5_001.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData5_002.csv
inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData5_003.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_001.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_002.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_003.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_001.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_002.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_003.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_001.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_002.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_003.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_001.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_002.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_003.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_001.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_002.csv
inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_003.csv
inst/extdata/mockData/steinbock/panel.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData1_001.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData1_002.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData1_003.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData2_001.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData2_002.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData2_003.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData3_001.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData3_002.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData3_003.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_001.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_002.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_003.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_001.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_002.csv
inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_003.csv
inst/extdata/mockData/steinbock/steinbock.sh
inst/extdata/mockData/tiffs/20210305_NE_mockData2_s0_a1_ac_fullFiltered.tiff
inst/extdata/spillover/Dy161.txt
inst/extdata/spillover/Dy162.txt
inst/extdata/spillover/Dy163.txt
inst/extdata/spillover/Dy164.txt
inst/scripts/download_TestData_cpout.Rmd
inst/scripts/download_TestData_raw.Rmd
inst/scripts/download_TestData_steinbock.Rmd
inst/scripts/download_spillover.Rmd
man/aggregateNeighbors.Rd
man/binAcrossPixels.Rd
man/buildSpatialGraph.Rd
man/countInteractions.Rd
man/detectCommunity.Rd
man/detectSpatialContext.Rd
man/filterPixels.Rd
man/filterSpatialContext.Rd
man/findBorderCells.Rd
man/minDistToCells.Rd
man/patchDetection.Rd
man/patchSize.Rd
man/plotSpatial.Rd
man/plotSpatialContext.Rd
man/plotSpotHeatmap.Rd
man/readImagefromTXT.Rd
man/readSCEfromTXT.Rd
man/read_cpout.Rd
man/read_steinbock.Rd
man/show_cpout_features.Rd
man/testInteractions.Rd
tests/testthat.R
tests/testthat/test_aggregateNeighbors.R
tests/testthat/test_binAcrossPixels.R
tests/testthat/test_buildSpatialGraph.R
tests/testthat/test_countInteractions.R
tests/testthat/test_detectCommunity.R
tests/testthat/test_detectSpatialContext.R
tests/testthat/test_filterPixels.R
tests/testthat/test_filterSpatialContext.R
tests/testthat/test_findBorderCells.R
tests/testthat/test_integration_interactions.R
tests/testthat/test_minDistToCells.R
tests/testthat/test_patchDetection.R
tests/testthat/test_patchSize.R
tests/testthat/test_plotSpatial.R
tests/testthat/test_plotSpatialContext.R
tests/testthat/test_plotSpotHeatmap.R
tests/testthat/test_readImagefromTXT.R
tests/testthat/test_readSCEfromTXT.R
tests/testthat/test_read_cpout.R
tests/testthat/test_read_steinbock.R
tests/testthat/test_show_cpout_features.R
tests/testthat/test_testInteractions.R
vignettes/imcRtools.Rmd
vignettes/imcRtools_sticker.png
vignettes/library.bib
