spatialLIBD
spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
Bioconductor version: Release (3.20)
Inspect interactively the spatially-resolved transcriptomics data from the 10x Genomics Visium platform as well as data from the Maynard, Collado-Torres et al, Nature Neuroscience, 2021 project analyzed by Lieber Institute for Brain Development (LIBD) researchers and collaborators.
Author: Leonardo Collado-Torres [aut, cre] 
, Kristen R. Maynard [ctb] , Andrew E. Jaffe [ctb] , Brenda Pardo [ctb] , Abby Spangler [ctb] , Jesús Vélez Santiago [ctb] , Lukas M. Weber [ctb] , Louise Huuki-Myers [ctb] , Nicholas Eagles [ctb]
Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>
citation("spatialLIBD")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spatialLIBD")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("spatialLIBD")| Guide to Multi-Gene Plots | HTML | R Script |
| Guide to Spatial Registration | HTML | R Script |
| Introduction to spatialLIBD | HTML | R Script |
| Using spatialLIBD with 10x Genomics public datasets | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, PackageTypeData, SequencingData, SingleCellData, SpatialData, Tissue |
| Version | 1.18.0 |
| License | Artistic-2.0 |
| Depends | SpatialExperiment(>= 1.3.3), R (>= 3.6) |
| Imports | shiny, golem, ggplot2, cowplot, plotly, viridisLite, shinyWidgets, sessioninfo, grid, grDevices, methods, AnnotationHub, utils, png, scater, DT, ExperimentHub, RColorBrewer, SummarizedExperiment, stats, graphics, S4Vectors, IRanges, fields, benchmarkme, SingleCellExperiment, BiocFileCache, jsonlite, tibble, rtracklayer, Matrix, BiocGenerics, GenomicRanges, magick, paletteer, scuttle, edgeR, limma, statmod, MatrixGenerics, rlang, dplyr |
| System Requirements | |
| URL | https://github.com/LieberInstitute/spatialLIBD |
| Bug Reports | https://support.bioconductor.org/tag/spatialLIBD |
See More
| Suggests | knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr, DropletUtils |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | Banksy, BayesSpace, DESpace |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | spatialLIBD_1.18.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/spatialLIBD |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/spatialLIBD |
| Package Short Url | https://bioconductor.org/packages/spatialLIBD/ |
| Package Downloads Report | Download Stats |