Package: VisiumIO 1.3.1

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], Dario Righelli [aut, ctb], Helena Crowell [aut, ctb]

VisiumIO_1.3.1.tar.gz
VisiumIO_1.3.1.zip(r-4.5)VisiumIO_1.3.1.zip(r-4.4)VisiumIO_1.1.8.zip(r-4.3)
VisiumIO_1.3.1.tgz(r-4.4-any)VisiumIO_1.1.8.tgz(r-4.3-any)
VisiumIO_1.3.1.tar.gz(r-4.5-noble)VisiumIO_1.3.1.tar.gz(r-4.4-noble)
VisiumIO_1.3.1.tgz(r-4.4-emscripten)VisiumIO_1.1.8.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-1.3.0(bioc 3.21)VisiumIO-1.2.0(bioc 3.20)

software infrastructure dataimport singlecell spatial bioconductor-package genomics

4.92 score 11 scripts 126 downloads 8 exports 84 dependencies

Last updated 24 days agofrom:35ac77950e. Checks:OK: 3 NOTE: 2 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	OK	Oct 02 2024
R-4.3-mac	OK	Oct 02 2024

Exports:compareBarcodes import TENxSpatialCSV TENxSpatialList TENxSpatialParquet TENxVisium TENxVisiumHD 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 HDF5Array 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 rhdf5 rhdf5filters Rhdf5lib 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 Oct 31 2024.

Last update: 2024-10-17
Started: 2023-11-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compare barcodes between raw and filtered data	compareBarcodes
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
Represent and import spatial Parquet data from 10X Genomics	.TENxSpatialParquet import,TENxSpatialParquet,ANY,ANY-method TENxSpatialParquet TENxSpatialParquet-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 HD samples	.TENxVisiumHD import,TENxVisiumHD,ANY,ANY-method TENxVisiumHD TENxVisiumHD-class
A class to represent and import multiple Visium samples	.TENxVisiumList import,TENxVisiumList,ANY,ANY-method TENxVisiumList TENxVisiumList-class