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spatialLIBD
This is thereleased version of spatialLIBD; for the devel version, seespatialLIBD.
spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0003-2140-308X, Kristen R. Maynard [ctb] ORCID: 0000-0003-0031-8468, Andrew E. Jaffe [ctb] ORCID: 0000-0001-6886-1454, Brenda Pardo [ctb] ORCID: 0000-0001-8103-7136, Abby Spangler [ctb] ORCID: 0000-0002-0028-9348, Jesús Vélez Santiago [ctb] ORCID: 0000-0001-5128-3838, Lukas M. Weber [ctb] ORCID: 0000-0002-3282-1730, Louise Huuki-Myers [ctb] ORCID: 0000-0001-5148-3602, Nicholas Eagles [ctb] ORCID: 0000-0002-9808-5254
Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>
citation("spatialLIBD")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("spatialLIBD")For older versions of R, please refer to the appropriateBioconductor 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 | 1.22.0 |
| 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 |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | spatialLIBD_1.22.0.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 |