pachterlab/SpatialFeatureExperiment
Integrating SpatialExperiment with Simple Features in sf

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Search the pachterlab/SpatialFeatureExperiment package
Vignettes
Functions
539
Source code
64
Man pages
73
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pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf
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API

API for pachterlab/SpatialFeatureExperiment
Integrating SpatialExperiment with Simple Features in sf

Global functions
.GetSlotNames Source code
.add_side_inds Source code
.affine_ebi Source code
.ag Source code
.ag_r Source code
.aggregate_SFE Source code
.aggregate_num Source code
.aggregate_sample Source code
.aggregate_sample_cell Source code
.aggregate_sample_tx Source code
.annot_fun Source code
.annot_summ Source code
.bbox2sf Source code
.bbox_sample Source code
.bbox_sample_g Source code
.center_mv Source code
.check_annotgeometries Source code
.check_bbox Source code
.check_dimgeo_names Source code
.check_features Man page Source code
.check_geometries Source code
.check_graph_sample_id Source code
.check_graph_str Source code
.check_graphs Source code
.check_graphs_item Source code
.check_graphs_sample Source code
.check_rg Man page Source code
.check_rg_multi_sample Source code
.check_rg_sample_all Source code
.check_rg_setter Source code
.check_rg_type Source code
.check_sample_id Man page Source code
.check_st_valid Source code
.check_tx_file Source code
.check_vizgen_fns Source code
.check_xenium_fns Source code
.combine_attr_fd Source code
.combine_fd Source code
.combine_reduceddim_fd Source code
.combine_transforms Source code
.comp_graph_sample Source code
.comp_visium_graph Source code
.concat_annotgeometries Source code
.crop_geometry Source code
.crop_imgs Source code
.df2sf_check Source code
.df2sf_in_list Source code
.df2sf_linestring Source code
.df2sf_list Source code
.df2sf_point Source code
.df2sf_polygon Source code
.dg_key Source code
.dg_key2 Source code
.dgr_key Source code
.dnn_bioc Source code
.dnn_sfe Source code
.empty_dgc Source code
.ext_ Man page Source code
.fill_missing Source code
.filter_polygons Source code
.format_fd Source code
.g2nb_sfe Source code
.gabriel_sfe Source code
.getMeta Source code
.get_XOA_version Source code
.get_affine_mat Source code
.get_centroids Source code
.get_col_then_annot Source code
.get_full_ext Source code
.get_fullres_scale_factor Source code
.get_fullres_size Source code
.get_graphs Source code
.get_imgData Source code
.get_img_fun Source code
.get_img_idx Source code
.get_intdimdata_all Source code
.get_internal Source code
.get_internal_feature Source code
.get_internal_id Source code
.get_mv Source code
.get_rg_multi Source code
.get_row_angle Source code
.get_subset Source code
.get_vizgen_images Source code
.get_xenium_images Source code
.getfun Source code
.h52poly_fov Source code
.id2symbol Source code
.if_flip_img Source code
.initialize_intdimdata Source code
.initialize_spatialGraphs Source code
.intdimdata_partial_replace Source code
.is0 Source code
.is_de_facto_point Source code
.knn_bioc Source code
.knn_sfe Source code
.make_grid_samples Source code
.make_na_df Source code
.make_sql_query Source code
.margin_name Source code
.mirror Source code
.mols2geo Source code
.mols2geo_split Source code
.names_types Source code
.nb2listw Source code
.nb2listw.default Source code
.nb2listw_strip Source code
.nb2listwdist2 Source code
.nb2listwdist2.default Source code
.nb2listwdist2.nbdnn Source code
.nb2listwdist2.nbknn Source code
.no_raw_bytes Source code
.numeric2NA Source code
.onLoad Source code
.out_intdimdata_id Source code
.path_valid2 Source code
.pixel2micron Source code
.rawToChar_df Source code
.read10xVisium Source code
.read_tx_output Source code
.reconcile_cols Source code
.relative_sfe Source code
.resample_spat Source code Source code
.rm_empty_geometries Man page Source code
.rotate Source code
.rotation_mat Source code
.sc2cg Source code
.scale Source code
.scale_ext Source code
.set_col_then_annot Source code
.set_ext Source code
.set_geometry_localResults Source code
.set_graphs Source code
.set_intdimdata_all Source code
.set_intdimdata_id Source code
.set_internal Source code
.set_internal_feature Source code
.set_internal_id Source code
.setfun Source code
.seu_to_sfe Source code
.sg_r Source code
.shift_ext Source code
.soi_sfe Source code
.spe_to_sfe Source code
.subset_listw Source code
.symbol2id Man page Source code
.toExtImage Source code
.toExtImage2 Source code
.transform Source code
.transform_bbox Source code
.transform_geometry Source code
.transform_geometry.matrix Source code
.transform_geometry.sf Source code
.transform_geometry_fun Source code
.transform_geometry_sf Source code
.transform_img_sfe Source code
.transform_samples Source code
.translate_value Source code
.transpose Source code
.use_subid Source code
.use_z Source code
.valid_bbox Source code
.value2df Man page Source code
.warn_symbol_duplicate Man page Source code
.xdimfun Source code
.xdimstr Source code
BioFormatsImage Man page Source code
BioFormatsImage-class Man page
BioFormatsImage-getters Man page
ExtImage Man page Source code
ExtImage-class Man page
Img<- Man page
Img<-,SpatialExperiment-method Man page
ROIPoly Man page Source code
ROIPoly<- Man page
SFE-image Man page
SFE-transform Man page
SFEVersion Man page Source code
SpatRasterImage Man page Source code
SpatRasterImage-class Man page
SpatialFeatureExperiment Man page Source code
SpatialFeatureExperiment-class Man page
SpatialFeatureExperiment-coercion Man page
SpatialFeatureExperiment-subset Man page
[,SpatialFeatureExperiment,ANY,ANY,ANY-method Man page
`ROIPoly<-` Source code
`annotGraph<-` Source code
`annotGraphNames<-` Source code
`annotGraphs<-` Source code
`cellSeg<-` Source code
`centroids<-` Source code
`colFeatureData<-` Source code
`colGeometries<-` Source code
`colGeometry<-` Source code
`colGeometryNames<-` Source code
`colGraph<-` Source code
`colGraphNames<-` Source code
`colGraphs<-` Source code
`geometryFeatureData<-` Source code
`nucSeg<-` Source code
`reducedDimFeatureData<-` Source code
`rowGeometries<-` Source code
`rowGeometry<-` Source code
`rowGeometryNames<-` Source code
`rowGraph<-` Source code
`rowGraphNames<-` Source code
`rowGraphs<-` Source code
`spotPoly<-` Source code
`tissueBoundary<-` Source code
`txSpots<-` Source code
addImg,SpatialFeatureExperiment-method Man page
addSelectTx Man page Source code
addTxSpots Man page Source code
addTxTech Man page Source code
addVisiumSpotPoly Man page Source code
affine Man page Source code
affineImg Man page
affineImg,BioFormatsImage-method Man page
affineImg,ExtImage-method Man page
affineImg,SpatRasterImage-method Man page
affineImg,SpatialFeatureExperiment-method Man page
aggBboxes Man page Source code
aggregate,SpatialFeatureExperiment-method Man page
aggregateTx Man page Source code
aggregateTxTech Man page Source code
annotGeometries Man page
annotGeometries,SpatialFeatureExperiment-method Man page
annotGeometries<- Man page
annotGeometries<-,SpatialFeatureExperiment-method Man page
annotGeometry Man page
annotGeometry,SpatialFeatureExperiment-method Man page
annotGeometry<- Man page
annotGeometry<-,SpatialFeatureExperiment-method Man page
annotGeometryNames Man page
annotGeometryNames,SpatialFeatureExperiment-method Man page
annotGeometryNames<- Man page
annotGeometryNames<-,SpatialFeatureExperiment,character-method Man page
annotGraph Man page Source code
annotGraph<- Man page
annotGraphNames Man page Source code
annotGraphNames<- Man page
annotGraphs Man page Source code
annotGraphs<- Man page
annotNPred Man page Source code
annotOp Man page Source code
annotPred Man page Source code
annotSummary Man page Source code
bbox Man page
bbox,SpatialFeatureExperiment-method Man page
bbox_center Man page Source code
cbind,SpatialFeatureExperiment-method Man page
cellSeg Man page Source code
cellSeg<- Man page
centroids Man page Source code
centroids<- Man page
changeSampleIDs Man page Source code
colData Man page
colData<- Man page
colFeatureData Man page Source code
colGeometries Man page Source code
colGeometries<- Man page
colGeometry Man page Source code
colGeometry<- Man page
colGeometryNames Man page Source code
colGeometryNames<- Man page
colGraph Man page Source code
colGraph<- Man page
colGraphNames Man page Source code
colGraphNames<- Man page
colGraphs Man page Source code
colGraphs<- Man page
counts Man page
crop Man page Source code
cropImg Man page
cropImg,BioFormatsImage-method Man page
cropImg,ExtImage-method Man page
cropImg,SpatRasterImage-method Man page
df2sf Man page Source code
dim,BioFormatsImage-method Man page
dimGeometries Man page
dimGeometries,SpatialFeatureExperiment-method Man page
dimGeometries<- Man page
dimGeometries<-,SpatialFeatureExperiment-method Man page
dimGeometry Man page
dimGeometry,SpatialFeatureExperiment-method Man page
dimGeometry<- Man page
dimGeometry<-,SpatialFeatureExperiment-method Man page
dimGeometryNames Man page
dimGeometryNames,SpatialFeatureExperiment-method Man page
dimGeometryNames<- Man page
dimGeometryNames<-,SpatialFeatureExperiment,numeric,character-me Man page
ext Man page
ext,BioFormatsImage-method Man page
ext,ExtImage-method Man page
ext,SpatRasterImage-method Man page
ext<-,BioFormatsImage,numeric-method Man page
ext<-,ExtImage,numeric-method Man page
ext<-,SpatRasterImage,numeric-method Man page
findSpatialNeighbors Man page
findSpatialNeighbors,SpatialFeatureExperiment-method Man page
findVisiumGraph Man page Source code
findVisiumHDGraph Man page Source code
formatTxSpots Man page Source code
formatTxTech Man page Source code
gdalParquetAvailable Man page Source code
geometryFeatureData Man page Source code
getImg Man page
getParams Man page Source code
getPixelSize Man page Source code
getTechTxFields Man page Source code
imageIDs Man page Source code
imgData Man page
imgRaster Man page
imgRaster,BioFormatsImage-method Man page
imgRaster,ExtImage-method Man page
imgRaster,SpatRasterImage-method Man page
imgSource Man page
imgSource,BioFormatsImage-method Man page
imgSource,ExtImage-method Man page
imgSource,SpatRasterImage-method Man page
internal-Voyager Man page
isFull Man page
isFull,BioFormatsImage-method Man page
listw2sparse Man page Source code
localResult Man page
localResult,SpatialFeatureExperiment-method Man page
localResult<- Man page
localResult<-,SpatialFeatureExperiment-method Man page
localResultAttrs Man page
localResultAttrs,SpatialFeatureExperiment-method Man page
localResultFeatures Man page
localResultFeatures,SpatialFeatureExperiment-method Man page
localResultNames Man page
localResultNames,SpatialFeatureExperiment-method Man page
localResultNames<- Man page
localResultNames<-,SpatialFeatureExperiment,character-method Man page
localResults Man page
localResults,SpatialFeatureExperiment-method Man page
localResults<- Man page
localResults<-,SpatialFeatureExperiment-method Man page
logcounts Man page
mirror Man page Source code
mirrorImg Man page
mirrorImg,BioFormatsImage-method Man page
mirrorImg,ExtImage-method Man page
mirrorImg,SpatRasterImage-method Man page
mirrorImg,SpatialFeatureExperiment-method Man page
multi_listw2sparse Man page Source code
nucSeg Man page Source code
nucSeg<- Man page
origin Man page
origin,BioFormatsImage-method Man page
read10xVisiumSFE Man page Source code
readCosMX Man page Source code
readSelectTx Man page Source code
readVisiumHD Man page Source code
readVizgen Man page Source code
readXenium Man page Source code
reducedDim Man page
reducedDimFeatureData Man page Source code
reexports Man page
removeEmptySpace Man page Source code
rmvImg Man page
rotate Man page Source code
rotateImg Man page
rotateImg,BioFormatsImage-method Man page
rotateImg,ExtImage-method Man page
rotateImg,SpatRasterImage-method Man page
rotateImg,SpatialFeatureExperiment-method Man page
rowData Man page
rowFeatureData Man page Source code
rowGeometries Man page Source code
rowGeometries<- Man page
rowGeometry Man page Source code
rowGeometry<- Man page
rowGeometryNames Man page Source code
rowGeometryNames<- Man page
rowGraph Man page Source code
rowGraph<- Man page
rowGraphNames Man page Source code
rowGraphNames<- Man page
rowGraphs Man page Source code
rowGraphs<- Man page
sampleIDs Man page Source code
saveRDS,SpatialFeatureExperiment-method Man page
scale Man page Source code
scaleImg Man page
scaleImg,AlignedSpatialImage-method Man page
scaleImg,SpatialFeatureExperiment-method Man page
show,BioFormatsImage-method Man page
show,ExtImage-method Man page
show,SpatRasterImage-method Man page
show,SpatialFeatureExperiment-method Man page
spatialCoords Man page
spatialCoords<- Man page
spatialCoordsNames Man page
spatialGraph Man page
spatialGraph,SpatialFeatureExperiment-method Man page
spatialGraph<- Man page
spatialGraph<-,SpatialFeatureExperiment-method Man page
spatialGraphNames Man page
spatialGraphNames,SpatialFeatureExperiment,numeric-method Man page
spatialGraphNames<- Man page
spatialGraphNames<-,SpatialFeatureExperiment,numeric,ANY,charact Man page
spatialGraphs Man page
spatialGraphs,SpatialFeatureExperiment-method Man page
spatialGraphs<- Man page
spatialGraphs<-,SpatialFeatureExperiment-method Man page
splitByCol Man page
splitByCol,SpatialFeatureExperiment,list-method Man page
splitByCol,SpatialFeatureExperiment,sf-method Man page
splitByCol,SpatialFeatureExperiment,sfc-method Man page
splitContiguity Man page Source code
splitSamples Man page Source code
spotPoly Man page Source code
spotPoly<- Man page
st_any_intersects Man page Source code
st_any_pred Man page Source code
st_n_intersects Man page Source code
st_n_pred Man page Source code
tissueBoundary Man page Source code
tissueBoundary<- Man page
toExtImage Man page
toExtImage,BioFormatsImage-method Man page
toExtImage,SpatRasterImage-method Man page
toSpatRasterImage Man page
toSpatRasterImage,BioFormatsImage-method Man page
toSpatRasterImage,ExtImage-method Man page
toSpatialFeatureExperiment Man page
toSpatialFeatureExperiment,Seurat-method Man page
toSpatialFeatureExperiment,SingleCellExperiment-method Man page
toSpatialFeatureExperiment,SpatialExperiment-method Man page
transformation Man page
transformation,BioFormatsImage-method Man page
translate Man page Source code
translateImg Man page
translateImg,BioFormatsImage-method Man page
translateImg,ExtImage-method Man page
translateImg,SpatRasterImage-method Man page
translateImg,SpatialFeatureExperiment-method Man page
transpose Man page Source code
transposeImg Man page
transposeImg,BioFormatsImage-method Man page
transposeImg,ExtImage-method Man page
transposeImg,SpatRasterImage-method Man page
transposeImg,SpatialFeatureExperiment-method Man page
txSpots Man page Source code
txSpots<- Man page
unit Man page
unit,SpatialFeatureExperiment-method Man page
updateObject Man page
updateObject,SpatialFeatureExperiment-method Man page
visium_row_col Man page
pachterlab/SpatialFeatureExperiment documentation built on Jan. 29, 2025, 10:32 p.m.

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