ggspavis
This is the development version of ggspavis; for the stable release version, see ggspavis.
Visualization functions for spatial transcriptomics data
Bioconductor version: Development (3.24)
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]
, Helena L. Crowell [aut]
, Yixing E. Dong [aut]
Maintainer: Lukas M. Weber <weberlm3 at gmail.com>
citation("ggspavis")):
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("ggspavis")
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("ggspavis")| ggspavis overview | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DimensionReduction, GeneExpression, QualityControl, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.19.1 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | MIT + file LICENSE |
| 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 | GSVA, smoothclust, HCATonsilData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ggspavis_1.19.1.tar.gz |
| Windows Binary (x86_64) | ggspavis_1.19.1.zip |
| macOS Binary (big-sur-x86_64) | ggspavis_1.19.1.tgz |
| macOS Binary (sonoma-arm64) | ggspavis_1.19.1.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 |