spatialLIBD
spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
Bioconductor version: 3.23 · Package version: 1.24.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spatialLIBD")Details
| Maintainer | Leonardo Collado-Torres <lcolladotor@gmail.com> |
| Author | Leonardo Collado-Torres [aut, cre] (ORCID: <https://orcid.org/0000-0003-2140-308X>), Kristen R. Maynard [ctb] (ORCID: <https://orcid.org/0000-0003-0031-8468>), Andrew E. Jaffe [ctb] (ORCID: <https://orcid.org/0000-0001-6886-1454>), Brenda Pardo [ctb] (ORCID: <https://orcid.org/0000-0001-8103-7136>), Abby Spangler [ctb] (ORCID: <https://orcid.org/0000-0002-0028-9348>), Jesús Vélez Santiago [ctb] (ORCID: <https://orcid.org/0000-0001-5128-3838>), Lukas M. Weber [ctb] (ORCID: <https://orcid.org/0000-0002-3282-1730>), Louise Huuki-Myers [ctb] (ORCID: <https://orcid.org/0000-0001-5148-3602>), Nicholas Eagles [ctb] (ORCID: <https://orcid.org/0000-0002-9808-5254>) |
| License | Artistic-2.0 |
| URL | https://github.com/LieberInstitute/spatialLIBD |
| Bug Reports | https://support.bioconductor.org/tag/spatialLIBD |
| Downloads rank | 456 |
| Source branch | RELEASE_3_23 |
| biocViews | ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, PackageTypeData, SequencingData, SingleCellData, SpatialData, Tissue |
Download
Dependencies
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
Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr, DropletUtils, RColorBrewer
Reverse dependencies
Imports Me (2): DeconvoBuddies, visiumStitched
Suggests Me (5): Banksy, BatchSVG, BayesSpace, DESpace, GSVA