├── .github ├── .gitignore └── workflows │ ├── build-checks-devel.yml │ ├── build-checks-release.yml │ └── docs.yml ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── aggregateNeighbors.R ├── binAcrossPixels.R ├── buildSpatialGraph.R ├── countInteractions.R ├── detectCommunity.R ├── detectSpatialContext.R ├── distToCells.R ├── filterPixels.R ├── filterSpatialContext.R ├── findBorderCells.R ├── patchDetection.R ├── patchSize.R ├── plotInteractions.R ├── plotSpatial.R ├── plotSpatialContext.R ├── plotSpotHeatmap.R ├── readImagefromTXT.R ├── readSCEfromTIFF.R ├── readSCEfromTXT.R ├── read_cpout.R ├── read_steinbock.R ├── show_cpout_features.R ├── testInteractions.R ├── utils.R └── validityChecks.R ├── README.md ├── inst ├── CITATION ├── extdata │ ├── mockData │ │ ├── cpout │ │ │ ├── Experiment.csv │ │ │ ├── Image.csv │ │ │ ├── Object_relationships.csv │ │ │ ├── cell.csv │ │ │ ├── panel.csv │ │ │ ├── var_Image.csv │ │ │ └── var_cell.csv │ │ ├── raw │ │ │ ├── 20210305_NE_mockData2_ROI_001_1.txt │ │ │ ├── 20210305_NE_mockData2_ROI_002_2.txt │ │ │ └── 20210305_NE_mockData2_ROI_003_3.txt │ │ ├── steinbock │ │ │ ├── images.csv │ │ │ ├── intensities │ │ │ │ ├── 20210305_NE_mockData1_001.csv │ │ │ │ ├── 20210305_NE_mockData1_002.csv │ │ │ │ ├── 20210305_NE_mockData1_003.csv │ │ │ │ ├── 20210305_NE_mockData2_001.csv │ │ │ │ ├── 20210305_NE_mockData2_002.csv │ │ │ │ ├── 20210305_NE_mockData2_003.csv │ │ │ │ ├── 20210305_NE_mockData3_001.csv │ │ │ │ ├── 20210305_NE_mockData3_002.csv │ │ │ │ ├── 20210305_NE_mockData3_003.csv │ │ │ │ ├── 20210305_NE_mockData4_001.csv │ │ │ │ ├── 20210305_NE_mockData4_002.csv │ │ │ │ ├── 20210305_NE_mockData4_003.csv │ │ │ │ ├── 20210305_NE_mockData5_001.csv │ │ │ │ ├── 20210305_NE_mockData5_002.csv │ │ │ │ └── 20210305_NE_mockData5_003.csv │ │ │ ├── neighbors │ │ │ │ ├── 20210305_NE_mockData1_001.csv │ │ │ │ ├── 20210305_NE_mockData1_002.csv │ │ │ │ ├── 20210305_NE_mockData1_003.csv │ │ │ │ ├── 20210305_NE_mockData2_001.csv │ │ │ │ ├── 20210305_NE_mockData2_002.csv │ │ │ │ ├── 20210305_NE_mockData2_003.csv │ │ │ │ ├── 20210305_NE_mockData3_001.csv │ │ │ │ ├── 20210305_NE_mockData3_002.csv │ │ │ │ ├── 20210305_NE_mockData3_003.csv │ │ │ │ ├── 20210305_NE_mockData4_001.csv │ │ │ │ ├── 20210305_NE_mockData4_002.csv │ │ │ │ ├── 20210305_NE_mockData4_003.csv │ │ │ │ ├── 20210305_NE_mockData5_001.csv │ │ │ │ ├── 20210305_NE_mockData5_002.csv │ │ │ │ └── 20210305_NE_mockData5_003.csv │ │ │ ├── panel.csv │ │ │ ├── regionprops │ │ │ │ ├── 20210305_NE_mockData1_001.csv │ │ │ │ ├── 20210305_NE_mockData1_002.csv │ │ │ │ ├── 20210305_NE_mockData1_003.csv │ │ │ │ ├── 20210305_NE_mockData2_001.csv │ │ │ │ ├── 20210305_NE_mockData2_002.csv │ │ │ │ ├── 20210305_NE_mockData2_003.csv │ │ │ │ ├── 20210305_NE_mockData3_001.csv │ │ │ │ ├── 20210305_NE_mockData3_002.csv │ │ │ │ ├── 20210305_NE_mockData3_003.csv │ │ │ │ ├── 20210305_NE_mockData4_001.csv │ │ │ │ ├── 20210305_NE_mockData4_002.csv │ │ │ │ ├── 20210305_NE_mockData4_003.csv │ │ │ │ ├── 20210305_NE_mockData5_001.csv │ │ │ │ ├── 20210305_NE_mockData5_002.csv │ │ │ │ └── 20210305_NE_mockData5_003.csv │ │ │ └── steinbock.sh │ │ └── tiffs │ │ │ └── 20210305_NE_mockData2_s0_a1_ac_fullFiltered.tiff │ ├── spillover │ │ ├── Dy161.txt │ │ ├── Dy162.txt │ │ ├── Dy163.txt │ │ └── Dy164.txt │ └── spillover_tiff │ │ ├── images.csv │ │ ├── img │ │ ├── compensation_001.tiff │ │ ├── compensation_002.tiff │ │ ├── compensation_003.tiff │ │ └── compensation_004.tiff │ │ ├── panel.csv │ │ └── txt │ │ ├── 20210205_CompSlide_NSCLC_TMA_LC_Dy161_1.txt │ │ ├── 20210205_CompSlide_NSCLC_TMA_LC_Dy162_2.txt │ │ ├── 20210205_CompSlide_NSCLC_TMA_LC_Dy163_3.txt │ │ └── 20210205_CompSlide_NSCLC_TMA_LC_Dy164_4.txt └── scripts │ ├── download_TestData_cpout.Rmd │ ├── download_TestData_raw.Rmd │ ├── download_TestData_steinbock.Rmd │ └── download_spillover.Rmd ├── man ├── aggregateNeighbors.Rd ├── binAcrossPixels.Rd ├── buildSpatialGraph.Rd ├── countInteractions.Rd ├── detectCommunity.Rd ├── detectSpatialContext.Rd ├── distToCells.Rd ├── filterPixels.Rd ├── filterSpatialContext.Rd ├── findBorderCells.Rd ├── patchDetection.Rd ├── patchSize.Rd ├── plotInteractions.Rd ├── plotSpatial.Rd ├── plotSpatialContext.Rd ├── plotSpotHeatmap.Rd ├── readImagefromTXT.Rd ├── readSCEfromTIFF.Rd ├── readSCEfromTXT.Rd ├── read_cpout.Rd ├── read_steinbock.Rd ├── show_cpout_features.Rd └── testInteractions.Rd ├── tests ├── testthat.R └── testthat │ ├── test_aggregateNeighbors.R │ ├── test_binAcrossPixels.R │ ├── test_buildSpatialGraph.R │ ├── test_countInteractions.R │ ├── test_detectCommunity.R │ ├── test_detectSpatialContext.R │ ├── test_distToCells.R │ ├── test_filterPixels.R │ ├── test_filterSpatialContext.R │ ├── test_findBorderCells.R │ ├── test_integration_interactions.R │ ├── test_patchDetection.R │ ├── test_patchSize.R │ ├── test_plotInteractions.R │ ├── test_plotSpatial.R │ ├── test_plotSpatialContext.R │ ├── test_plotSpotHeatmap.R │ ├── test_readImagefromTXT.R │ ├── test_readSCEfromTIFF.R │ ├── test_readSCEfromTXT.R │ ├── test_read_cpout.R │ ├── test_read_steinbock.R │ ├── test_show_cpout_features.R │ └── test_testInteractions.R └── vignettes ├── imcRtools.Rmd ├── imcRtools_sticker.png └── library.bib /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- /.github/workflows/build-checks-devel.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/.github/workflows/build-checks-devel.yml -------------------------------------------------------------------------------- /.github/workflows/build-checks-release.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/.github/workflows/build-checks-release.yml -------------------------------------------------------------------------------- /.github/workflows/docs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/.github/workflows/docs.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.DS_Store 2 | */._* 3 | *.html 4 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/NEWS -------------------------------------------------------------------------------- /R/aggregateNeighbors.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/aggregateNeighbors.R -------------------------------------------------------------------------------- /R/binAcrossPixels.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/binAcrossPixels.R -------------------------------------------------------------------------------- /R/buildSpatialGraph.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/buildSpatialGraph.R -------------------------------------------------------------------------------- /R/countInteractions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/countInteractions.R -------------------------------------------------------------------------------- /R/detectCommunity.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/detectCommunity.R -------------------------------------------------------------------------------- /R/detectSpatialContext.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/detectSpatialContext.R -------------------------------------------------------------------------------- /R/distToCells.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/distToCells.R -------------------------------------------------------------------------------- /R/filterPixels.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/filterPixels.R -------------------------------------------------------------------------------- /R/filterSpatialContext.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/filterSpatialContext.R -------------------------------------------------------------------------------- /R/findBorderCells.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/findBorderCells.R -------------------------------------------------------------------------------- /R/patchDetection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/patchDetection.R -------------------------------------------------------------------------------- /R/patchSize.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/patchSize.R -------------------------------------------------------------------------------- /R/plotInteractions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/plotInteractions.R -------------------------------------------------------------------------------- /R/plotSpatial.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/plotSpatial.R -------------------------------------------------------------------------------- /R/plotSpatialContext.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/plotSpatialContext.R -------------------------------------------------------------------------------- /R/plotSpotHeatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/plotSpotHeatmap.R -------------------------------------------------------------------------------- /R/readImagefromTXT.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/readImagefromTXT.R -------------------------------------------------------------------------------- /R/readSCEfromTIFF.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/readSCEfromTIFF.R -------------------------------------------------------------------------------- /R/readSCEfromTXT.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/readSCEfromTXT.R -------------------------------------------------------------------------------- /R/read_cpout.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/read_cpout.R -------------------------------------------------------------------------------- /R/read_steinbock.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/read_steinbock.R -------------------------------------------------------------------------------- /R/show_cpout_features.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/show_cpout_features.R -------------------------------------------------------------------------------- /R/testInteractions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/testInteractions.R -------------------------------------------------------------------------------- /R/utils.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/utils.R -------------------------------------------------------------------------------- /R/validityChecks.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/R/validityChecks.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/README.md -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/CITATION -------------------------------------------------------------------------------- /inst/extdata/mockData/cpout/Experiment.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/cpout/Experiment.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/cpout/Image.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/cpout/Image.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/cpout/Object_relationships.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/cpout/Object_relationships.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/cpout/cell.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/cpout/cell.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/cpout/panel.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/cpout/panel.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/cpout/var_Image.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/cpout/var_Image.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/cpout/var_cell.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/cpout/var_cell.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/raw/20210305_NE_mockData2_ROI_001_1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/raw/20210305_NE_mockData2_ROI_001_1.txt -------------------------------------------------------------------------------- /inst/extdata/mockData/raw/20210305_NE_mockData2_ROI_002_2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/raw/20210305_NE_mockData2_ROI_002_2.txt -------------------------------------------------------------------------------- /inst/extdata/mockData/raw/20210305_NE_mockData2_ROI_003_3.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/raw/20210305_NE_mockData2_ROI_003_3.txt -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/images.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/images.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData1_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData1_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData1_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData1_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData1_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData1_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData2_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData2_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData2_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData2_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData2_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData2_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData3_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData3_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData3_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData3_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData3_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData3_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData4_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData4_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData4_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData4_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData4_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData4_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData5_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData5_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData5_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData5_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData5_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData5_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/panel.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/panel.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData1_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData1_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData1_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData1_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData1_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData1_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData2_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData2_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData2_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData2_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData2_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData2_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData3_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData3_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData3_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData3_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData3_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData3_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_001.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_001.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_002.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_002.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_003.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_003.csv -------------------------------------------------------------------------------- /inst/extdata/mockData/steinbock/steinbock.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/steinbock/steinbock.sh -------------------------------------------------------------------------------- /inst/extdata/mockData/tiffs/20210305_NE_mockData2_s0_a1_ac_fullFiltered.tiff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/mockData/tiffs/20210305_NE_mockData2_s0_a1_ac_fullFiltered.tiff -------------------------------------------------------------------------------- /inst/extdata/spillover/Dy161.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover/Dy161.txt -------------------------------------------------------------------------------- /inst/extdata/spillover/Dy162.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover/Dy162.txt -------------------------------------------------------------------------------- /inst/extdata/spillover/Dy163.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover/Dy163.txt -------------------------------------------------------------------------------- /inst/extdata/spillover/Dy164.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover/Dy164.txt -------------------------------------------------------------------------------- /inst/extdata/spillover_tiff/images.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover_tiff/images.csv -------------------------------------------------------------------------------- /inst/extdata/spillover_tiff/img/compensation_001.tiff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover_tiff/img/compensation_001.tiff -------------------------------------------------------------------------------- /inst/extdata/spillover_tiff/img/compensation_002.tiff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover_tiff/img/compensation_002.tiff -------------------------------------------------------------------------------- /inst/extdata/spillover_tiff/img/compensation_003.tiff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover_tiff/img/compensation_003.tiff -------------------------------------------------------------------------------- /inst/extdata/spillover_tiff/img/compensation_004.tiff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover_tiff/img/compensation_004.tiff -------------------------------------------------------------------------------- /inst/extdata/spillover_tiff/panel.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover_tiff/panel.csv -------------------------------------------------------------------------------- /inst/extdata/spillover_tiff/txt/20210205_CompSlide_NSCLC_TMA_LC_Dy161_1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover_tiff/txt/20210205_CompSlide_NSCLC_TMA_LC_Dy161_1.txt -------------------------------------------------------------------------------- /inst/extdata/spillover_tiff/txt/20210205_CompSlide_NSCLC_TMA_LC_Dy162_2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover_tiff/txt/20210205_CompSlide_NSCLC_TMA_LC_Dy162_2.txt -------------------------------------------------------------------------------- /inst/extdata/spillover_tiff/txt/20210205_CompSlide_NSCLC_TMA_LC_Dy163_3.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover_tiff/txt/20210205_CompSlide_NSCLC_TMA_LC_Dy163_3.txt -------------------------------------------------------------------------------- /inst/extdata/spillover_tiff/txt/20210205_CompSlide_NSCLC_TMA_LC_Dy164_4.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/extdata/spillover_tiff/txt/20210205_CompSlide_NSCLC_TMA_LC_Dy164_4.txt -------------------------------------------------------------------------------- /inst/scripts/download_TestData_cpout.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/scripts/download_TestData_cpout.Rmd -------------------------------------------------------------------------------- /inst/scripts/download_TestData_raw.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/scripts/download_TestData_raw.Rmd -------------------------------------------------------------------------------- /inst/scripts/download_TestData_steinbock.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/scripts/download_TestData_steinbock.Rmd -------------------------------------------------------------------------------- /inst/scripts/download_spillover.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/inst/scripts/download_spillover.Rmd -------------------------------------------------------------------------------- /man/aggregateNeighbors.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/aggregateNeighbors.Rd -------------------------------------------------------------------------------- /man/binAcrossPixels.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/binAcrossPixels.Rd -------------------------------------------------------------------------------- /man/buildSpatialGraph.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/buildSpatialGraph.Rd -------------------------------------------------------------------------------- /man/countInteractions.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/countInteractions.Rd -------------------------------------------------------------------------------- /man/detectCommunity.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/detectCommunity.Rd -------------------------------------------------------------------------------- /man/detectSpatialContext.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/detectSpatialContext.Rd -------------------------------------------------------------------------------- /man/distToCells.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/distToCells.Rd -------------------------------------------------------------------------------- /man/filterPixels.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/filterPixels.Rd -------------------------------------------------------------------------------- /man/filterSpatialContext.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/filterSpatialContext.Rd -------------------------------------------------------------------------------- /man/findBorderCells.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/findBorderCells.Rd -------------------------------------------------------------------------------- /man/patchDetection.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/patchDetection.Rd -------------------------------------------------------------------------------- /man/patchSize.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/patchSize.Rd -------------------------------------------------------------------------------- /man/plotInteractions.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/plotInteractions.Rd -------------------------------------------------------------------------------- /man/plotSpatial.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/plotSpatial.Rd -------------------------------------------------------------------------------- /man/plotSpatialContext.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/plotSpatialContext.Rd -------------------------------------------------------------------------------- /man/plotSpotHeatmap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/plotSpotHeatmap.Rd -------------------------------------------------------------------------------- /man/readImagefromTXT.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/readImagefromTXT.Rd -------------------------------------------------------------------------------- /man/readSCEfromTIFF.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/readSCEfromTIFF.Rd -------------------------------------------------------------------------------- /man/readSCEfromTXT.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/readSCEfromTXT.Rd -------------------------------------------------------------------------------- /man/read_cpout.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/read_cpout.Rd -------------------------------------------------------------------------------- /man/read_steinbock.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/read_steinbock.Rd -------------------------------------------------------------------------------- /man/show_cpout_features.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/show_cpout_features.Rd -------------------------------------------------------------------------------- /man/testInteractions.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/man/testInteractions.Rd -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/test_aggregateNeighbors.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_aggregateNeighbors.R -------------------------------------------------------------------------------- /tests/testthat/test_binAcrossPixels.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_binAcrossPixels.R -------------------------------------------------------------------------------- /tests/testthat/test_buildSpatialGraph.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_buildSpatialGraph.R -------------------------------------------------------------------------------- /tests/testthat/test_countInteractions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_countInteractions.R -------------------------------------------------------------------------------- /tests/testthat/test_detectCommunity.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_detectCommunity.R -------------------------------------------------------------------------------- /tests/testthat/test_detectSpatialContext.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_detectSpatialContext.R -------------------------------------------------------------------------------- /tests/testthat/test_distToCells.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_distToCells.R -------------------------------------------------------------------------------- /tests/testthat/test_filterPixels.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_filterPixels.R -------------------------------------------------------------------------------- /tests/testthat/test_filterSpatialContext.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_filterSpatialContext.R -------------------------------------------------------------------------------- /tests/testthat/test_findBorderCells.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_findBorderCells.R -------------------------------------------------------------------------------- /tests/testthat/test_integration_interactions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_integration_interactions.R -------------------------------------------------------------------------------- /tests/testthat/test_patchDetection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_patchDetection.R -------------------------------------------------------------------------------- /tests/testthat/test_patchSize.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_patchSize.R -------------------------------------------------------------------------------- /tests/testthat/test_plotInteractions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_plotInteractions.R -------------------------------------------------------------------------------- /tests/testthat/test_plotSpatial.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_plotSpatial.R -------------------------------------------------------------------------------- /tests/testthat/test_plotSpatialContext.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_plotSpatialContext.R -------------------------------------------------------------------------------- /tests/testthat/test_plotSpotHeatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_plotSpotHeatmap.R -------------------------------------------------------------------------------- /tests/testthat/test_readImagefromTXT.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_readImagefromTXT.R -------------------------------------------------------------------------------- /tests/testthat/test_readSCEfromTIFF.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_readSCEfromTIFF.R -------------------------------------------------------------------------------- /tests/testthat/test_readSCEfromTXT.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_readSCEfromTXT.R -------------------------------------------------------------------------------- /tests/testthat/test_read_cpout.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_read_cpout.R -------------------------------------------------------------------------------- /tests/testthat/test_read_steinbock.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_read_steinbock.R -------------------------------------------------------------------------------- /tests/testthat/test_show_cpout_features.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_show_cpout_features.R -------------------------------------------------------------------------------- /tests/testthat/test_testInteractions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/tests/testthat/test_testInteractions.R -------------------------------------------------------------------------------- /vignettes/imcRtools.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/vignettes/imcRtools.Rmd -------------------------------------------------------------------------------- /vignettes/imcRtools_sticker.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/vignettes/imcRtools_sticker.png -------------------------------------------------------------------------------- /vignettes/library.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/imcRtools/HEAD/vignettes/library.bib --------------------------------------------------------------------------------