ggspavis
This is thereleased version of ggspavis; for the devel version, seeggspavis.
Visualization functions for spatial transcriptomics data
Bioconductor version: Release (3.22)
Visualization functions for spatial transcriptomics data. Includes functions to generate several types of plots, including spot plots, feature (molecule) plots, reduced dimension plots, spot-level quality control (QC) plots, and feature-level QC plots, for datasets from the 10x Genomics Visium and other technological platforms. Datasets are assumed to be in either SpatialExperiment or SingleCellExperiment format.
Author: Lukas M. Weber [aut, cre]
ORCID: 0000-0002-3282-1730, Helena L. Crowell [aut] ORCID: 0000-0002-4801-1767, Yixing E. Dong [aut] ORCID: 0009-0003-5115-5686
Maintainer: Lukas M. Weber <lmweb012 at gmail.com>
citation("ggspavis")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("ggspavis")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("ggspavis")| ggspavis overview | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DimensionReduction,GeneExpression,QualityControl,SingleCell,Software,Spatial,Transcriptomics |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 years) |
| License | MIT + fileLICENSE |
| Depends | ggplot2 |
| Imports | SpatialExperiment,SingleCellExperiment,SummarizedExperiment,ggside, grid,ggrepel,RColorBrewer,scales, grDevices, methods, stats |
| System Requirements | |
| URL | https://github.com/lmweber/ggspavis |
| Bug Reports | https://github.com/lmweber/ggspavis/issues |
See More
| Suggests | BiocStyle,rmarkdown,knitr,OSTA.data,VisiumIO,arrow,STexampleData,BumpyMatrix,scater,scran,uwot,testthat,patchwork |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA |
| Suggests Me | smoothclust,HCATonsilData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | ggspavis_1.16.0.tar.gz |
| Windows Binary (x86_64) | ggspavis_1.16.0.zip |
| macOS Binary (x86_64) | ggspavis_1.16.0.tgz |
| macOS Binary (arm64) | ggspavis_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ggspavis |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ggspavis |
| Bioc Package Browser | https://code.bioconductor.org/browse/ggspavis/ |
| Package Short Url | https://bioconductor.org/packages/ggspavis/ |
| Package Downloads Report | Download Stats |