Files in pachterlab/SpatialFeatureExperiment
Integrating SpatialExperiment with Simple Features in sf
.Rbuildignore
.covrignore
.github/.gitignore
.github/CONTRIBUTING
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/pkgdown_dev.yml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/AllGenerics.R
R/SFE-class.R
R/aggregate.R
R/align.R
R/annotGeometries.R
R/cbind.R
R/changeSampleIDs.R
R/coerce.R
R/data.R
R/df2sf.R
R/dimGeometries.R
R/featureData.R
R/formatTxSpots.R
R/geometry_operation.R
R/graph_wrappers.R
R/image.R
R/int_dimData.R
R/internal-Voyager.R
R/listw2sparse.R
R/localResults.R
R/read.R
R/reexports.R
R/saveRDS.R
R/spatialGraphs.R
R/split.R
R/subset.R
R/sysdata.rda
R/transformation.R
R/updateObject.R
R/utils.R
R/validity.R
R/zzz.R
README.md
_pkgdown.yml
data-raw/polyt.tif
data-raw/sfe_schematics.odg
data/visium_row_col.rda
inst/CITATION
inst/extdata/ag.rds
inst/extdata/ag_samples.rds
inst/extdata/annotgraph1.rds
inst/extdata/annotgraph2.rds
inst/extdata/cg_toy.rds
inst/extdata/cg_toy2.rds
inst/extdata/colgraph1.rds
inst/extdata/colgraph2.rds
inst/extdata/colgraph_visium.rds
inst/extdata/colgraph_visium2.rds
inst/extdata/colgraph_visium_sub.rds
inst/extdata/contiguity.rds
inst/extdata/ls_df.rds
inst/extdata/ls_df_singleton.rds
inst/extdata/ls_sf.rds
inst/extdata/ls_sf_singleton.rds
inst/extdata/mpol_df.rds
inst/extdata/mpol_sf.rds
inst/extdata/multils_df.rds
inst/extdata/multils_sf.rds
inst/extdata/multipts_df.rds
inst/extdata/multipts_df_wrong_sample.rds
inst/extdata/multipts_sf.rds
inst/extdata/pieces.rds
inst/extdata/pol_df.rds
inst/extdata/pol_sf.rds
inst/extdata/pts_df.rds
inst/extdata/pts_sf.rds
inst/extdata/pts_sf_dia.rds
inst/extdata/sample01/outs/filtered_feature_bc_matrix/barcodes.tsv
inst/extdata/sample01/outs/filtered_feature_bc_matrix/features.tsv
inst/extdata/sample01/outs/filtered_feature_bc_matrix/matrix.mtx
inst/extdata/sample01/outs/spatial/aligned_fiducials.jpg
inst/extdata/sample01/outs/spatial/barcode_fluorescence_intensity.csv
inst/extdata/sample01/outs/spatial/detected_tissue_image.jpg
inst/extdata/sample01/outs/spatial/scalefactors_json.json
inst/extdata/sample01/outs/spatial/spatial_enrichment.csv
inst/extdata/sample01/outs/spatial/tissue_hires_image.png
inst/extdata/sample01/outs/spatial/tissue_lowres_image.png
inst/extdata/sample01/outs/spatial/tissue_positions.csv
inst/extdata/sample02/outs/filtered_feature_bc_matrix/barcodes.tsv
inst/extdata/sample02/outs/filtered_feature_bc_matrix/features.tsv
inst/extdata/sample02/outs/filtered_feature_bc_matrix/matrix.mtx
inst/extdata/sample02/outs/spatial/aligned_fiducials.jpg
inst/extdata/sample02/outs/spatial/barcode_fluorescence_intensity.csv
inst/extdata/sample02/outs/spatial/detected_tissue_image.jpg
inst/extdata/sample02/outs/spatial/scalefactors_json.json
inst/extdata/sample02/outs/spatial/spatial_enrichment.csv
inst/extdata/sample02/outs/spatial/tissue_hires_image.png
inst/extdata/sample02/outs/spatial/tissue_lowres_image.png
inst/extdata/sample02/outs/spatial/tissue_positions.csv
inst/extdata/seu_vis_toy.rds
inst/extdata/seu_vis_toy_multi.rds
inst/extdata/sfe_multi_sample.rds
inst/extdata/sfe_old_spi.rds
inst/extdata/sfe_toy.rds
inst/extdata/sfe_visium.rds
inst/extdata/subpieces.rds
inst/script/sfe_old_spi.R
inst/script/spaceranger_toy.R
inst/script/test_rowgeometry.R
inst/script/testdata_Geometries.R
inst/script/testdata_Graphs.R
inst/script/testdata_df2sf.R
inst/script/testdata_graph_wrappers.R
inst/script/testdata_split.R
inst/script/visium_row_col.R
man/BioFormatsImage-getters.Rd
man/BioFormatsImage.Rd
man/ExtImage.Rd
man/Img-set-SpatialExperiment-method.Rd
man/SFE-image.Rd
man/SFE-transform.Rd
man/SpatRasterImage.Rd
man/SpatialFeatureExperiment-class.Rd
man/SpatialFeatureExperiment-coercion.Rd
man/SpatialFeatureExperiment-subset.Rd
man/SpatialFeatureExperiment.Rd
man/addVisiumSpotPoly.Rd
man/affineImg.Rd
man/aggBboxes.Rd
man/aggregate-SpatialFeatureExperiment-method.Rd
man/aggregateTx.Rd
man/annotGeometries.Rd
man/annotOp.Rd
man/annotPred.Rd
man/annotSummary.Rd
man/bbox-SpatialFeatureExperiment-method.Rd
man/bbox_center.Rd
man/cbind-SpatialFeatureExperiment-method.Rd
man/changeSampleIDs.Rd
man/colFeatureData.Rd
man/colGeometries.Rd
man/crop.Rd
man/cropImg.Rd
man/df2sf.Rd
man/dim-BioFormatsImage-method.Rd
man/dimGeometries.Rd
man/ext.Rd
man/findSpatialNeighbors-SpatialFeatureExperiment-method.Rd
man/findVisiumGraph.Rd
man/findVisiumHDGraph.Rd
man/formatTxSpots.Rd
man/formatTxTech.Rd
man/gdalParquetAvailable.Rd
man/getParams.Rd
man/getPixelSize.Rd
man/getTechTxFields.Rd
man/imageIDs.Rd
man/imgRaster.Rd
man/imgSource.Rd
man/internal-Voyager.Rd
man/listw2sparse.Rd
man/localResults.Rd
man/mirrorImg.Rd
man/multi_listw2sparse.Rd
man/read10xVisiumSFE.Rd
man/readCosMX.Rd
man/readSelectTx.Rd
man/readVisiumHD.Rd
man/readVizgen.Rd
man/readXenium.Rd
man/reexports.Rd
man/removeEmptySpace.Rd
man/rotateImg.Rd
man/rowGeometries.Rd
man/sampleIDs.Rd
man/saveRDS-SpatialFeatureExperiment-method.Rd
man/scaleImg.Rd
man/show-SpatialFeatureExperiment-method.Rd
man/spatialGraphs.Rd
man/splitByCol.Rd
man/st_any_pred.Rd
man/toExtImage.Rd
man/toSpatRasterImage.Rd
man/translateImg.Rd
man/transposeImg.Rd
man/unit-SpatialFeatureExperiment-method.Rd
man/updateObject.Rd
man/visium_row_col.Rd
tests/testthat.R
tests/testthat/test-SFE-class.R
tests/testthat/test-aggregate.R
tests/testthat/test-annotGeometries.R
tests/testthat/test-cbind.R
tests/testthat/test-coerce.R
tests/testthat/test-df2sf.R
tests/testthat/test-dimGeometries.R
tests/testthat/test-featureData.R
tests/testthat/test-formatTxSpots.R
tests/testthat/test-geometry_operation.R
tests/testthat/test-graph_wrappers.R
tests/testthat/test-image.R
tests/testthat/test-internal-Voyager.R
tests/testthat/test-listw2sparse.R
tests/testthat/test-localResults.R
tests/testthat/test-read.R
tests/testthat/test-saveRDS.R
tests/testthat/test-spatialGraphs.R
tests/testthat/test-split.R
tests/testthat/test-subset.R
tests/testthat/test-updateObject.R
tests/testthat/test-utils.R
tests/testthat/test-validity.R
vignettes/.gitignore
vignettes/SFE.Rmd
vignettes/sfe_schematics.png
