Package: visiumStitched 0.99.15

Nicholas J. Eagles

visiumStitched: Enable downstream analysis of Visium capture areas stitched together with Fiji

This package provides helper functions for working with multiple Visium capture areas that overlap each other. This package was developed along with the companion example use case data available from https://github.com/LieberInstitute/visiumStitched_brain. visiumStitched prepares SpaceRanger (10x Genomics) output files so you can stitch the images from groups of capture areas together with Fiji. Then visiumStitched builds a SpatialExperiment object with the stitched data and makes an artificial hexogonal grid enabling the seamless use of spatial clustering methods that rely on such grid to identify neighboring spots, such as PRECAST and BayesSpace. The SpatialExperiment objects created by visiumStitched are compatible with spatialLIBD, which can be used to build interactive websites for stitched SpatialExperiment objects. visiumStitched also enables casting SpatialExperiment objects as Seurat objects.

Authors:Nicholas J. Eagles [aut, cre], Leonardo Collado-Torres [ctb]

visiumStitched_0.99.15.tar.gz
visiumStitched_0.99.15.zip(r-4.5)visiumStitched_0.99.15.zip(r-4.4)
visiumStitched_0.99.15.tgz(r-4.4-any)
visiumStitched_0.99.15.tar.gz(r-4.5-noble)visiumStitched_0.99.15.tar.gz(r-4.4-noble)
visiumStitched_0.99.15.tgz(r-4.4-emscripten)
visiumStitched.pdf |visiumStitched.html
visiumStitched/json (API)
NEWS

# Install 'visiumStitched' in R:
install.packages('visiumStitched', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lieberinstitute/visiumstitched/issues

On BioConductor:visiumStitched-0.99.15(bioc 3.21)

softwarespatialtranscriptomicstranscriptiongeneexpressionvisualizationdataimport10xgenomicsbioconductorspatial-transcriptomicsspatialexperimentspatiallibdvisium

5.38 score 1 stars 4 scripts 33 downloads 8 exports 217 dependencies

Last updated 1 months agofrom:4c5401969b. Checks:4 OK, 1 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 13 2025
R-4.5-winOKJan 13 2025
R-4.5-linuxOKJan 13 2025
R-4.4-winOKJan 13 2025
R-4.4-macERRORJan 13 2025

Exports:add_array_coordsadd_overlap_infoas.Seuratbuild_SpatialExperimentmerge_overlappingprep_fiji_coordsprep_fiji_imagerescale_fiji_inputs

Dependencies:abindAnnotationDbiAnnotationHubaskpassassertthatassortheadattemptbase64encbeachmatbeeswarmbenchmarkmebenchmarkmeDataBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocNeighborsBiocParallelBiocSingularBiocVersionBiostringsbitbit64bitopsblobbmpbslibcachemCairoclicliprcodetoolscolorspacecommonmarkconfigcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdoParalleldotCall64downloaderdplyrdqrngDropletUtilsDTedgeRevaluateExperimentHubfansifarverfastmapfieldsfilelockFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegolemgridExtragtableHDF5ArrayherehighrhmshtmltoolshtmlwidgetshttpuvhttrigraphimagerIRangesirlbaisobanditeratorsjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagickmagrittrmapsMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpaletteerpheatmappillarpkgcondpkgconfigplogrplotlypngprettyunitsprismaticprogresspromisespurrrR.methodsS3R.ooR.utilsR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRCurlreadbitmapreadrrematch2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrprojrootRsamtoolsRSpectraRSQLiterstudioapirsvdrtracklayerRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscuttlesessioninfoshinyshinyWidgetsSingleCellExperimentsitmosnowsourcetoolsspamSparseArraysparseMatrixStatsSpatialExperimentspatialLIBDstatmodstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttifftinytextzdbUCSC.utilsutf8uwotvctrsviporviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzlibbioc

Introduction to visiumStitched

Rendered fromvisiumStitched.Rmdusingknitr::rmarkdownon Jan 13 2025.

Last update: 2024-10-24
Started: 2024-05-22

Miscellaneous notes

Rendered frommisc.Rmdusingknitr::rmarkdownon Jan 13 2025.

Last update: 2024-10-24
Started: 2024-07-30