Package: TENxXeniumData 1.8.0

Matineh Rahmatbakhsh

TENxXeniumData: Collection of Xenium spatial data by 10X genomics

Collection of Xenium spatial transcriptomics datasets provided by 10x Genomics, formatted into the Bioconductor classes, the SpatialExperiment or SpatialFeatureExperiment (SFE), to facilitate seamless integration into various applications, including examples, demonstrations, and tutorials. The constructed data objects include gene expression profiles, per-transcript location data, centroid, segmentation boundaries (e.g., cell or nucleus boundaries), and image.

Authors:Matineh Rahmatbakhsh [aut, cre], Monica Ge [aut]

TENxXeniumData_1.8.0.tar.gz
TENxXeniumData_1.8.0.tar.gz(r-4.7-any)TENxXeniumData_1.8.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
TENxXeniumData/json (API)

# Install 'TENxXeniumData' in R:

install.packages('TENxXeniumData', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mrbakhsh/tenxxeniumdata/issues

On BioConductor:TENxXeniumData-1.9.0(data/experiment 3.24)TENxXeniumData-1.8.0(data/experiment 3.23)

experimentdata experimenthub spatialdata datapkg

4.48 score 3 stars 2 scripts 4 exports 161 dependencies

Last updated from:a89c0e6d95 (on RELEASE_3_23). Checks:3 NOTE, 1 OK. Indexed: no.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	NOTE	214
linux-devel	NOTE	581
source / vignettes	OK	347
linux-release	NOTE	441

Exports:sfe_human_pancreas sfe_mouse_brain spe_human_pancreas spe_mouse_brain

Dependencies:abind AnnotationDbi AnnotationHub askpass assorthead backports base64enc beachmat BH Biobase BiocBaseUtils BiocFileCache BiocGenerics biocmake BiocManager BiocNeighbors BiocParallel BiocVersion Biostrings bit bit64 bitops blob boot bslib BumpyMatrix cachem checkmate class classInt cli coda codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir digest dir.expiry dplyr dqrng DropletUtils e1071 EBImage edgeR evaluate ExperimentHub fastmap fftwtools filelock fontawesome formatR Formula fs futile.logger futile.options generics GenomicRanges geometries glue h5mread HDF5Array highr htmltools htmlwidgets httr httr2 insight IRanges jpeg jquerylib jsonlite KEGGREST KernSmooth knitr lambda.r lattice LearnBayes lifecycle limma locfit magick magrittr marginaleffects MASS Matrix MatrixGenerics matrixStats memoise mime multcomp mvtnorm nlme openssl pillar pkgconfig png proxy purrr R.methodsS3 R.oo R.utils R6 rappdirs Rcpp RCurl rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown RSQLite s2 S4Arrays S4Vectors sandwich sass scuttle Seqinfo sf sfheaders SingleCellExperiment sitmo snow sp SparseArray sparseMatrixStats SpatialExperiment SpatialFeatureExperiment spatialreg spData spdep statmod stringi stringr SummarizedExperiment survival sys terra TH.data tibble tidyr tidyselect tiff tinytex units utf8 vctrs withr wk xfun XVector yaml zeallot zoo

TENxXeniumData

Introduction | Installation | Available datasets | Loading the data | Session information

Rendered fromTENxXeniumData.Rmdusingknitr::rmarkdown

Last update: 2024-02-04
Started: 2024-02-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
TENxXeniumData	sfe_human_pancreas sfe_mouse_brain spe_human_pancreas spe_mouse_brain TENxXeniumData