Files in gusef/IrisSpatialFeatures
A package to extract spatial features based on multiplex IF images
.Rbuildignore
.gitignore
DESCRIPTION
Dockerfile
IrisSpatialFeatures.Rproj
LICENSE
NAMESPACE
R/IrisSpatialFeatures.R
R/RcppExports.R
R/classes.R
R/counting.functions.R
R/data.R
R/feature.selection.R
R/interactions.analysis.R
R/nearest.neighbor.R
R/neighborhood.analysis.R
R/normalized.nearest.neighbor.R
R/permute.R
R/plotting.functions.R
R/proximity.analysis.R
R/proximity.fraction.analysis.R
R/read.functions.R
R/threshold.functions.R
R/transform.functions.R
README.md
data/IrisSpatialFeatures_data.RData
inst/NEWS
inst/doc/IrisSpatialFeatures.pdf
inst/extdata/MEL2/MEL2_080416_2_Invasive_Margin.tif
inst/extdata/MEL2/MEL2_080416_2_Tumor.tif
inst/extdata/MEL2/MEL2_080416_2_cell_seg_data.txt
inst/extdata/MEL2/MEL2_080416_2_cell_seg_data_summary.txt
inst/extdata/MEL2/MEL2_080416_2_memb_seg_map.tif
inst/extdata/MEL2/MEL2_080416_2_score_data.txt
inst/extdata/MEL2/MEL2_080416_7_Invasive_Margin.tif
inst/extdata/MEL2/MEL2_080416_7_Tumor.tif
inst/extdata/MEL2/MEL2_080416_7_cell_seg_data.txt
inst/extdata/MEL2/MEL2_080416_7_cell_seg_data_summary.txt
inst/extdata/MEL2/MEL2_080416_7_memb_seg_map.tif
inst/extdata/MEL2/MEL2_080416_7_score_data.txt
inst/extdata/MEL3/MEL3_120116_1_Invasive_Margin.tif
inst/extdata/MEL3/MEL3_120116_1_Tumor.tif
inst/extdata/MEL3/MEL3_120116_1_cell_seg_data.txt
inst/extdata/MEL3/MEL3_120116_1_cell_seg_data_summary.txt
inst/extdata/MEL3/MEL3_120116_1_memb_seg_map.tif
inst/extdata/MEL3/MEL3_120116_1_score_data.txt
inst/extdata/MEL3/MEL3_120116_2_Invasive_Margin.tif
inst/extdata/MEL3/MEL3_120116_2_Tumor.tif
inst/extdata/MEL3/MEL3_120116_2_cell_seg_data.txt
inst/extdata/MEL3/MEL3_120116_2_cell_seg_data_summary.txt
inst/extdata/MEL3/MEL3_120116_2_memb_seg_map.tif
inst/extdata/MEL3/MEL3_120116_2_score_data.txt
man/Coordinate-class.Rd
man/ImageSet-class.Rd
man/IrisSpatialFeatures-package.Rd
man/IrisSpatialFeatures_data.Rd
man/NNN-class.Rd
man/NNN_Compare-class.Rd
man/Sample-class.Rd
man/aggregated_nn_data_frame.Rd
man/as.data.frame.Rd
man/binned_gated_nn_data_frame.Rd
man/collapse_markers.Rd
man/compare_normalized_nearest_neighbor.Rd
man/counts_data_frame.Rd
man/counts_per_mm2_data_frame.Rd
man/counts_per_mm2_sample_data_frame.Rd
man/counts_sample_data_frame.Rd
man/extract_ROI.Rd
man/extract_features.Rd
man/extract_interactions.Rd
man/extract_mask.Rd
man/extract_nearest_neighbor.Rd
man/extract_proximity.Rd
man/feature_selection.Rd
man/get_all_interactions.Rd
man/get_all_nearest_neighbors.Rd
man/get_all_proximities.Rd
man/get_count_ratios.Rd
man/get_counts_per_mm2.Rd
man/get_counts_per_mm2_noncollapsed.Rd
man/get_interactions.Rd
man/get_nearest_neighbors.Rd
man/get_proximities.Rd
man/interaction_counts_data_frame.Rd
man/interaction_counts_sample_data_frame.Rd
man/interaction_maps.Rd
man/interaction_permutation_test.Rd
man/interaction_proportion_comparison_permutation_test.Rd
man/interaction_proportion_data_frame.Rd
man/interactions_sample_data_frame.Rd
man/multiple_proximity_sample_data_frame.Rd
man/neighbor_ray_plot.Rd
man/nn.test.Rd
man/nn_comparison_dataframe.Rd
man/nn_comparison_permutation_test.Rd
man/nn_data_frame.Rd
man/normal_nearest_neighbor.Rd
man/normal_nearest_neighbor_sample.Rd
man/normal_nearest_neighbor_sample_once.Rd
man/overview_plot.Rd
man/plot.Rd
man/plot_interactions.Rd
man/plot_nearest_neighbor.Rd
man/plot_nnn.Rd
man/plot_proximities.Rd
man/proximity_sample_data_frame.Rd
man/raw_data-class.Rd
man/rayplot_single_coordinate.Rd
man/read_raw.Rd
man/shuffle_labels.Rd
man/threshold_dataset.Rd
src/RcppExports.cpp
src/interaction.cpp
src/masking.cpp
tests/testthat.R
tests/testthat/test-workflow.R
vignettes/IrisSpatialFeatures.Rmd
