concordexR

This is the development version of concordexR; for the stable release version, see concordexR.

Identify Spatial Homogeneous Regions with concordex

Bioconductor version: Development (3.23)

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, enter citation("concordexR")):

Installation

To install this package, start R (version "4.6") 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.

Documentation


Reference Manual	PDF

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Details

biocViews	Clustering, SingleCell, Software, Spatial, Transcriptomics
Version	1.9.1
In Bioconductor since	BioC 3.17 (R-4.3) (2.5 years)
License	Artistic-2.0
Depends	R (>= 4.5.0)
Imports	BiocGenerics, BiocNeighbors, BiocParallel, bluster, cli, DelayedArray, Matrix, methods, purrr, rlang, SingleCellExperiment, sparseMatrixStats, SpatialExperiment, SummarizedExperiment
System Requirements
URL	https://github.com/pachterlab/concordexR https://pachterlab.github.io/concordexR/
Bug Reports	https://github.com/pachterlab/concordexR/issues

Suggests	BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans, patchwork, rmarkdown, scater, SFEData, SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/concordexR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/concordexR
Package Short Url	https://bioconductor.org/packages/concordexR/
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