pachterlab/SpatialFeatureExperiment
Integrating SpatialExperiment with Simple Features in sf

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Search the pachterlab/SpatialFeatureExperiment package
Vignettes
Functions
358
Source code
48
Man pages
33
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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
.ag Source code
.ag_r Source code
.annot_fun Source code
.annot_summ Source code
.bbox_sample Source code
.check_annotgeometries 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_sample_id Man page Source code
.comp_graph_sample Source code
.comp_visium_graph Source code
.concat_annotgeometries Source code
.crop_geometry Source code
.crop_imgs Source code
.df2poly_mat 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
.df_split_sample_id Source code
.dg_key Source code
.dg_key2 Source code
.dgr_key Source code
.dnn_bioc Source code
.dnn_sfe Source code
.fill_missing Source code
.filter_polygons Source code
.g2nb_sfe Source code
.gabriel_sfe Source code
.get_centroids Source code
.get_col_then_annot Source code
.get_graphs Source code
.get_imgData Source code
.get_intdimdata_all Source code
.get_internal_feature Source code
.get_internal_id Source code
.getfun Source code
.h52poly_fov Source code
.if_flip_img Source code
.initialize_intdimdata Source code
.initialize_spatialGraphs Source code
.intdimdata_partial_replace Source code
.is_de_facto_point Source code
.knn_bioc Source code
.knn_sfe Source code
.make_na_df Source code
.margin_len_fun Source code
.margin_name Source code
.margin_num 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
.out_intdimdata_id Source code
.pixel2micron Source code
.reconcile_cols Source code
.relative_sfe Source code
.rm_empty_geometries Man page Source code
.sc2cg Source code
.set_col_then_annot Source code
.set_geometry_localResults Source code
.set_graphs Source code
.set_intdimdata_all Source code
.set_intdimdata_id Source code
.set_internal_feature Source code
.set_internal_id Source code
.setfun Source code
.sg_r Source code
.soi_sfe Source code
.spe_to_sfe Source code
.symbol2id Man page Source code
.transform Source code
.transform_samples Source code
.translate Source code
.translate_value Source code
.value2df Man page Source code
.warn_symbol_duplicate Man page Source code
.xdimfun Source code
.xdimstr Source code
ROIPoly Man page Source code
ROIPoly<- Man page
SFE-image Man page
SFE-transform Man page
SFEVersion 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
`cellSeg<-` Source code
`centroids<-` Source code
`colGeometries<-` Source code
`colGeometry<-` Source code
`colGeometryNames<-` Source code
`colGraph<-` Source code
`colGraphNames<-` Source code
`nucSeg<-` Source code
`rowGeometries<-` Source code
`rowGeometry<-` Source code
`rowGeometryNames<-` Source code
`rowGraph<-` Source code
`rowGraphNames<-` Source code
`spotPoly<-` Source code
`tissueBoundary<-` Source code
`txSpots<-` Source code
addImg,SpatialFeatureExperiment-method Man page
addVisiumSpotPoly 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,character-method Man page
annotGeometry,SpatialFeatureExperiment,missing-method Man page
annotGeometry,SpatialFeatureExperiment,numeric-method Man page
annotGeometry<- Man page
annotGeometry<-,SpatialFeatureExperiment,character-method Man page
annotGeometry<-,SpatialFeatureExperiment,missing-method Man page
annotGeometry<-,SpatialFeatureExperiment,numeric-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
annotGraphs,SpatialFeatureExperiment,character,character-method Man page
annotGraphs,SpatialFeatureExperiment,character,missing-method Man page
annotGraphs,SpatialFeatureExperiment,missing,missing-method Man page
annotGraphs<- Man page
annotGraphs<-,SpatialFeatureExperiment,character,character-metho Man page
annotGraphs<-,SpatialFeatureExperiment,character,missing-method Man page
annotGraphs<-,SpatialFeatureExperiment,missing,missing-method 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
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
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
colGraphs,SpatialFeatureExperiment,character,character-method Man page
colGraphs,SpatialFeatureExperiment,character,missing-method Man page
colGraphs,SpatialFeatureExperiment,missing,missing-method Man page
colGraphs<- Man page
colGraphs<-,SpatialFeatureExperiment,character,character-method Man page
colGraphs<-,SpatialFeatureExperiment,character,missing-method Man page
colGraphs<-,SpatialFeatureExperiment,missing,missing-method Man page
crop Man page Source code
df2sf Man page Source code
dimGeometries Man page
dimGeometries,SpatialFeatureExperiment-method Man page
dimGeometries<- Man page
dimGeometries<-,SpatialFeatureExperiment-method Man page
dimGeometry Man page
dimGeometry,SpatialFeatureExperiment,character-method Man page
dimGeometry,SpatialFeatureExperiment,missing-method Man page
dimGeometry,SpatialFeatureExperiment,numeric-method Man page
dimGeometry<- Man page
dimGeometry<-,SpatialFeatureExperiment,character-method Man page
dimGeometry<-,SpatialFeatureExperiment,missing-method Man page
dimGeometry<-,SpatialFeatureExperiment,numeric-method Man page
dimGeometryNames Man page
dimGeometryNames,SpatialFeatureExperiment-method Man page
dimGeometryNames<- Man page
dimGeometryNames<-,SpatialFeatureExperiment,numeric,character-me Man page
findSpatialNeighbors Man page
findSpatialNeighbors,SpatialFeatureExperiment-method Man page
findVisiumGraph Man page Source code
getImg Man page
imgData Man page
imgRaster,SpatRasterImage-method Man page
imgSource,SpatRasterImage-method Man page
internal-Voyager Man page
localResult Man page
localResult,SpatialFeatureExperiment,character-method Man page
localResult,SpatialFeatureExperiment,missing-method Man page
localResult,SpatialFeatureExperiment,numeric-method Man page
localResult<- Man page
localResult<-,SpatialFeatureExperiment,character-method Man page
localResult<-,SpatialFeatureExperiment,missing-method Man page
localResult<-,SpatialFeatureExperiment,numeric-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,ANY,character-method Man page
localResults,SpatialFeatureExperiment,missing,missing-method Man page
localResults<- Man page
localResults<-,SpatialFeatureExperiment,ANY,character-method Man page
localResults<-,SpatialFeatureExperiment,missing,missing-method Man page
mirror Man page Source code
mirrorImg,SpatRasterImage-method Man page
mirrorImg,SpatialFeatureExperiment-method Man page
nucSeg Man page Source code
nucSeg<- Man page
read10xVisiumSFE Man page Source code
readVizgen Man page Source code
reexports Man page
removeEmptySpace Man page Source code
rowData Man page
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
rowGraphs,SpatialFeatureExperiment,character,character-method Man page
rowGraphs,SpatialFeatureExperiment,character,missing-method Man page
rowGraphs,SpatialFeatureExperiment,missing,missing-method Man page
rowGraphs<- Man page
rowGraphs<-,SpatialFeatureExperiment,character,character-method Man page
rowGraphs<-,SpatialFeatureExperiment,character,missing-method Man page
rowGraphs<-,SpatialFeatureExperiment,missing,missing-method Man page
sampleIDs Man page Source code
saveRDS,SpatialFeatureExperiment-method Man page
show,SpatialFeatureExperiment-method Man page
spatialCoords Man page
spatialCoords<- Man page
spatialCoordsNames Man page
spatialGraph Man page
spatialGraph,SpatialFeatureExperiment,character,numeric-method Man page
spatialGraph,SpatialFeatureExperiment,missing,numeric-method Man page
spatialGraph,SpatialFeatureExperiment,numeric,numeric-method Man page
spatialGraph<- Man page
spatialGraph<-,SpatialFeatureExperiment,character,numeric-method Man page
spatialGraph<-,SpatialFeatureExperiment,missing,numeric-method Man page
spatialGraph<-,SpatialFeatureExperiment,numeric,numeric-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,missing,character,missing Man page
spatialGraphs,SpatialFeatureExperiment,missing,missing,missing-m Man page
spatialGraphs,SpatialFeatureExperiment,numeric,character,charact Man page
spatialGraphs,SpatialFeatureExperiment,numeric,character,missing Man page
spatialGraphs,SpatialFeatureExperiment,numeric,missing,missing-m Man page
spatialGraphs<- Man page
spatialGraphs<-,SpatialFeatureExperiment,missing,character,missi Man page
spatialGraphs<-,SpatialFeatureExperiment,missing,missing,missing Man page
spatialGraphs<-,SpatialFeatureExperiment,numeric,NULL,missing-me Man page
spatialGraphs<-,SpatialFeatureExperiment,numeric,character,chara Man page
spatialGraphs<-,SpatialFeatureExperiment,numeric,character,missi Man page
spatialGraphs<-,SpatialFeatureExperiment,numeric,missing,missing Man page
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
toSpatialFeatureExperiment Man page
toSpatialFeatureExperiment,SingleCellExperiment-method Man page
toSpatialFeatureExperiment,SpatialExperiment-method Man page
transpose Man page Source code
transposeImg 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 March 11, 2024, 11:11 p.m.

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