Package: VisiumIO 1.1.0

Marcel Ramos

VisiumIO: Import Visium data from the 10X Space Ranger pipeline

The package allows users to readily import spatial data obtained from either the 10X website or from the Space Ranger pipeline. Supported formats include tar.gz, h5, and mtx files. Multiple files can be imported at once with *List type of functions. The package represents data mainly as SpatialExperiment objects.

Authors:Marcel Ramos [aut, cre]

VisiumIO_1.1.0.tar.gz
VisiumIO_1.1.0.zip(r-4.5)VisiumIO_1.1.0.zip(r-4.4)VisiumIO_1.1.0.zip(r-4.3)
VisiumIO_1.1.0.tgz(r-4.4-any)VisiumIO_1.1.0.tgz(r-4.3-any)
VisiumIO_1.1.0.tar.gz(r-4.5-noble)VisiumIO_1.1.0.tar.gz(r-4.4-noble)
VisiumIO_1.1.0.tgz(r-4.4-emscripten)VisiumIO_1.1.0.tgz(r-4.3-emscripten)
VisiumIO.pdf |VisiumIO.html✨
VisiumIO/json (API)
NEWS

# Install 'VisiumIO' in R:

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

Bug tracker:https://github.com/waldronlab/visiumio/issues

On BioConductor:VisiumIO-1.1.0(bioc 3.20)VisiumIO-1.0.0(bioc 3.19)

bioconductor-package

5 exports 0.71 score 80 dependencies

Last updated 2 months agofrom:212381ff63

Exports:import TENxSpatialCSV TENxSpatialList TENxVisium TENxVisiumList

Dependencies:abind askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO bit bit64 bitops blob cachem cli clipr cpp11 crayon curl DBI dbplyr DelayedArray dplyr fansi fastmap filelock generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue hms httr IRanges jsonlite lattice lifecycle magick magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr prettyunits progress purrr R.methodsS3 R.oo R.utils R6 Rcpp RCurl readr rjson rlang RSQLite S4Arrays S4Vectors SingleCellExperiment SparseArray SpatialExperiment stringi stringr SummarizedExperiment sys TENxIO tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs vroom withr XVector zlibbioc

VisiumIO: Import 10X Genomics Visium Experiment Data

Marcel Ramos

Rendered fromVisiumIO.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-12-13
Started: 2023-11-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Represent and import spatial CSV data from 10X Genomics	.TENxSpatialCSV import,TENxSpatialCSV,ANY,ANY-method TENxSpatialCSV TENxSpatialCSV-class
A class to represent and import spatial Visium data	.TENxSpatialList import,TENxSpatialList,ANY,ANY-method TENxSpatialList TENxSpatialList-class
A class to represent and import a single Visium Sample	.TENxVisium import,TENxVisium,ANY,ANY-method TENxVisium TENxVisium-class
A class to represent and import multiple Visium samples	.TENxVisiumList import,TENxVisiumList,ANY,ANY-method TENxVisiumList TENxVisiumList-class