Package: SpatialOmicsOverlay 1.5.0
Maddy Griswold
SpatialOmicsOverlay: Spatial Overlay for Omic Data from Nanostring GeoMx Data
Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.
Authors:
SpatialOmicsOverlay_1.5.0.tar.gz
SpatialOmicsOverlay_1.5.0.zip(r-4.5)SpatialOmicsOverlay_1.5.0.zip(r-4.4)SpatialOmicsOverlay_1.5.0.zip(r-4.3)
SpatialOmicsOverlay_1.5.0.tgz(r-4.4-any)SpatialOmicsOverlay_1.5.0.tgz(r-4.3-any)
SpatialOmicsOverlay_1.5.0.tar.gz(r-4.4-noble)
SpatialOmicsOverlay_1.5.0.tgz(r-4.4-emscripten)
SpatialOmicsOverlay.pdf |SpatialOmicsOverlay.html✨
SpatialOmicsOverlay/json (API)
NEWS
| # Install 'SpatialOmicsOverlay' in R: |
| install.packages('SpatialOmicsOverlay', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:SpatialOmicsOverlay-1.5.0(bioc 3.20)SpatialOmicsOverlay-1.4.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:7b62e7e471
Exports:add4ChannelImageaddImageFileaddImageOmeTiffaddPlottingFactorbookendStrchangeColoringIntensitychangeImageColoringcheckValidRescoordscreateCoordFilecreateMaskcropSamplescropTissuedownloadMouseBrainImageflipXflipYfluorfluorLegendimageInfolabWorkmetamoveCoordsoutlineoverlayparseOverlayAttrsparseScanMetadataplotFactorsplotSpatialOverlaypositionreadLabWorksheetreadSpatialOverlayrecolorremoveSampleressampNamesscaleBarRatioscaledscanMetasegshowshowImageslideNameSpatialOverlayspatialPosSpatialPositionworkflowxmlExtraction
Dependencies:abindaskpassbackportsbase64encbeeswarmBiobaseBiocFileCacheBiocGenericsBiostringsbitbit64bitopsblobbootbroombroom.helpersbslibcachemcellrangerclicliprcodetoolscolorspacecommonmarkcpp11crayoncurldata.tableDBIdbplyrdigestdotCall64dplyrEBImageEnvStatsevaluatefansifarverfastmapfftwtoolsfilelockfontawesomeforcatsfsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGeomxToolsGGallyggbeeswarmggiraphggplot2ggstatsggtextggthemesglobalsgluegridtextgtablehavenhighrhmshtmltoolshtmlwidgetshttrIRangesisobandjpegjquerylibjsonliteknitrlabelinglabelledlatticelifecyclelistenvlme4lmerTestlocfitmagickmagrittrmarkdownMASSMatrixmemoisemgcvmimeminqamunsellNanoStringNCToolsnlmenloptrnortestnumDerivopensslparallellypatchworkpbapplypheatmappillarpkgconfigplogrplotrixplyrpngprettyunitsprogressprogressrpurrrR6rappdirsRBioFormatsRColorBrewerRcppRcppEigenRCurlreadrreadxlrematchreshape2rJavarjsonrlangrmarkdownRSQLiteS4VectorssassscalesscattermoreSeuratObjectspspamstringistringrsyssystemfontstibbletidyrtidyselecttifftinytextzdbUCSC.utilsutf8uuidvctrsviporviridisLitevroomwithrxfunXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add 4-channel image to SpatialOverlay from OME-TIFF. Allows for recoloring of image | add4ChannelImage |
| Add image to SpatialOverlay from disk | addImageFile |
| Add image to SpatialOverlay from OME-TIFF | addImageOmeTiff |
| Add plotting factor to 'SpatialOverlay' object | addPlottingFactor addPlottingFactor,character-method addPlottingFactor,data.frame-method addPlottingFactor,factor-method addPlottingFactor,matrix-method addPlottingFactor,NanoStringGeoMxSet-method addPlottingFactor,numeric-method addPlottingFactor,tbl-method addPlottingFactor,tbl_df-method |
| Match ROIs in annotation file to xml | annotMatching |
| Print long string in more managable fashion | bookendStr |
| Update color intensities for changing to RGB image | changeColoringIntensity |
| Update color scheme for changing to RGB image | changeImageColoring |
| Determine lowest resolution image in OME-TIFF | checkValidRes |
| Create coordinate file for entire scan | createCoordFile |
| Create a binary mask from a base 64 string | createMask |
| Crop to zoom in on given ROIs | cropSamples |
| Crop to remove black boundary around tissue. | cropTissue |
| Download Mouse Brain OME-TIFF from NanoString's Spatial Organ Atlas | downloadMouseBrainImage |
| Flip x axis in image and overlay points | flipX |
| Flip y axis in image and overlay points | flipY |
| Add legend of fluorescence targets that make up image | fluorLegend |
| Move coordinates if they don't match image | moveCoords |
| Parse the xml file for AOI attributes in GeoMx images | parseOverlayAttrs |
| Parse the xml file for the scan metadata of GeoMx images | parseScanMetadata |
| overlay plots | plotSpatialOverlay |
| Read lab worksheet into dataframe of annotations | readLabWorksheet |
| Read in 'SpatialOverlay' from tiff file and annotations | readSpatialOverlay |
| recolor images after changing colors and/or color intensities | recolor |
| Remove sample(s) from SpatialOverlay | removeSample |
| Class to Contain NanoString Spatial Overlay Images and Data | class:SpatialOverlay coords coords,SpatialOverlay-method fluor fluor,SpatialOverlay-method imageInfo imageInfo,SpatialOverlay-method labWork labWork,SpatialOverlay-method outline outline,SpatialOverlay-method overlay overlay,SpatialOverlay-method plotFactors plotFactors,SpatialOverlay-method res res,SpatialOverlay-method sampNames sampNames,SpatialOverlay-method scaleBarRatio scaleBarRatio,SpatialOverlay-method scaled scaled,SpatialOverlay-method scanMeta scanMeta,SpatialOverlay-method seg seg,SpatialOverlay-method show,SpatialOverlay-method showImage showImage,SpatialOverlay-method slideName slideName,SpatialOverlay-method SpatialOverlay SpatialOverlay,character-method SpatialOverlay-class workflow workflow,SpatialOverlay-method |
| Class to Contain NanoString Spatial Overlay ROI information | class:SpatialPosition meta meta,SpatialPosition-method position position,SpatialPosition-method show,SpatialPosition-method spatialPos spatialPos,SpatialPosition-method SpatialPosition SpatialPosition,data.frame-method SpatialPosition,environment-method SpatialPosition,matrix-method SpatialPosition,missing-method SpatialPosition-class |
| Extract xml from OME-TIFF | xmlExtraction |
