spatialLIBD

DOI:10.18129/B9.bioc.spatialLIBD

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, seespatialLIBD.

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

Bioconductor version: 3.14

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]

Maintainer: Leonardo Collado-Torres

Installation

To install this package, start R (version "4.1") 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

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("spatialLIBD")

HTML	R Script	Introduction to spatialLIBD
HTML	R Script	Using spatialLIBD with 10x Genomics public datasets
PDF		Reference Manual
Text		NEWS

Details

biocViews	ExperimentData,ExperimentHub,ExpressionData,Homo_sapiens_Data,PackageTypeData,SequencingData,SingleCellData,Tissue
Version	1.6.5
License	Artistic-2.0
Depends	SpatialExperiment(>= 1.3.3), R (>= 3.6)
Imports	shiny,golem,ggplot2,cowplot,plotly,viridisLite,shinyWidgets,Polychrome,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
LinkingTo
Suggests	knitr,RefManageR,rmarkdown,BiocStyle,testthat(>= 2.1.0),covr,here,BiocManager,pryr
SystemRequirements
Enhances
URL	https://github.com/LieberInstitute/spatialLIBD
BugReports	https://support.bioconductor.org/t/spatialLIBD
Depends On Me
Imports Me
Suggests Me	BayesSpace
Links To Me
Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	spatialLIBD_1.6.5.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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	//www.andersvercelli.com/packages/spatialLIBD/
Package Downloads Report	Download Stats