DESpace
This is the released version of DESpace; for the devel version, see DESpace.
DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions
Bioconductor version: Release (3.23)
Intuitive framework for identifying spatially variable genes (SVGs) and differential spatial variable pattern (DSP) between conditions via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. For multi-sample, multi-condition datasets, we again fit a NB model via edgeR, incorporating spatial clusters, conditions and their interactions as covariates. DSP genes-representing differences in spatial gene expression patterns across experimental conditions-are identified by testing the interaction between spatial clusters and conditions.
Author: Peiying Cai [aut, cre]
, Simone Tiberi [aut]
Maintainer: Peiying Cai <peiying.cai at uzh.ch>
citation("DESpace")):
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")
BiocManager::install("DESpace")
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("DESpace")| A framework to discover spatially variable genes | HTML | R Script |
| Differential Spatial Pattern between conditions | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Spatial, StatisticalMethod, Transcriptomics, Visualization |
| Version | 2.4.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | edgeR, limma, dplyr, stats, Matrix, SpatialExperiment, ggplot2, SummarizedExperiment, S4Vectors, BiocGenerics, data.table, assertthat, terra, sf, spatstat.explore, spatstat.geom, ggforce, ggnewscale, patchwork, BiocParallel, methods, scales, scuttle |
| System Requirements | |
| URL | https://github.com/peicai/DESpace https://peicai.github.io/DESpace/ |
| Bug Reports | https://github.com/peicai/DESpace/issues |
See More
| Suggests | knitr, rmarkdown, testthat, BiocStyle, muSpaData, ExperimentHub, spatialLIBD, purrr, reshape2, tidyverse, concaveman |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DESpace_2.4.0.tar.gz |
| Windows Binary (x86_64) | DESpace_2.4.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | DESpace_2.4.0.tgz |
| macOS Binary (sonoma-arm64) | DESpace_2.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DESpace |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DESpace |
| Bioc Package Browser | https://code.bioconductor.org/browse/DESpace/ |
| Package Short Url | https://bioconductor.org/packages/DESpace/ |
| Package Downloads Report | Download Stats |