spatialLIBD
This is the development version of spatialLIBD; for the stable release version, see spatialLIBD.
spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.25.2 |
| License | Artistic-2.0 |
| Depends | SpatialExperiment(>= 1.3.3), R (>= 4.1) |
| Imports | shiny, golem, ggplot2, cowplot, plotly, viridisLite, shinyWidgets, sessioninfo, grid, grDevices, methods, AnnotationHub, utils, png, scater, DT, ExperimentHub, SummarizedExperiment, stats, graphics, S4Vectors, IRanges, benchmarkme, SingleCellExperiment, BiocFileCache, jsonlite, tibble, rtracklayer, Matrix, BiocGenerics, GenomicRanges, magick, paletteer, scuttle, edgeR, limma, statmod, MatrixGenerics, rlang, dplyr, ComplexHeatmap, circlize |
| 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, RColorBrewer |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | DeconvoBuddies, visiumStitched, OSTA |
| Suggests Me | Banksy, BatchSVG, BayesSpace, DESpace, GSVA |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | spatialLIBD_1.25.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-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 |