This is the development version of concordexR; for the stable release version, see concordexR.
Identify Spatial Homogeneous Regions with concordexBioconductor version: Development (3.22)
Spatial homogeneous regions (SHRs) in tissues are domains that are homogenous with respect to cell type composition. We present a method for identifying SHRs using spatial transcriptomics data, and demonstrate that it is efficient and effective at finding SHRs for a wide variety of tissue types. concordex relies on analysis of k-nearest-neighbor (kNN) graphs. The tool is also useful for analysis of non-spatial transcriptomics data, and can elucidate the extent of concordance between partitions of cells derived from clustering algorithms, and transcriptomic similarity as represented in kNN graphs.
Author: Kayla Jackson [aut, cre] ORCID: 0000-0001-6483-0108 , A. Sina Booeshaghi [aut] ORCID: 0000-0002-6442-4502 , Angel Galvez-Merchan [aut] ORCID: 0000-0001-7420-8697 , Lambda Moses [aut] ORCID: 0000-0002-7092-9427 , Alexandra Kim [ctb], Laura Luebbert [ctb] ORCID: 0000-0003-1379-2927 , Lior Pachter [aut, rev, ths] ORCID: 0000-0002-9164-6231
Maintainer: Kayla Jackson <kaylajac at caltech.edu>
Citation (from within R, entercitation("concordexR")): 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("concordexR")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("concordexR")Follow Installation instructions to use this package in your R session.
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