scider
This is the development version of scider; for the stable release version, see scider.
Spatial cell-type inter-correlation by density in R
Bioconductor version: Development (3.22)
scider is an user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.
Author: Mengbo Li [aut]
, Ning Liu [aut]
, Quoc Hoang Nguyen [aut]
, Yunshun Chen [aut, cre]
Maintainer: Yunshun Chen <yuchen at wehi.edu.au>
citation("scider")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("scider")
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("scider")| scider_introduction | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Software, Spatial, Transcriptomics |
| Version | 1.7.1 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.3) |
| Imports | SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, SpatialPack, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, isoband, S4Vectors, grDevices, dbscan, hexDensity, hexbin, uwot, SingleCellExperiment, BiocNeighbors, irlba |
| System Requirements | |
| URL | https://github.com/ChenLaboratory/scider https://chenlaboratory.github.io/scider/ |
| Bug Reports | https://github.com/ChenLaboratory/scider/issues |
See More
| Suggests | edgeR, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scider_1.7.1.tar.gz |
| Windows Binary (x86_64) | scider_1.7.0.zip (64-bit only) |
| macOS Binary (x86_64) | scider_1.7.0.tgz |
| macOS Binary (arm64) | scider_1.7.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scider |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scider |
| Bioc Package Browser | https://code.bioconductor.org/browse/scider/ |
| Package Short Url | https://bioconductor.org/packages/scider/ |
| Package Downloads Report | Download Stats |