Package: concordexR 1.13.0

Kayla Jackson

concordexR: Identify Spatial Homogeneous Regions with concordex

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.

Authors:Kayla Jackson [aut, cre], A. Sina Booeshaghi [aut], Angel Galvez-Merchan [aut], Lambda Moses [aut], Alexandra Kim [ctb], Laura Luebbert [ctb], Lior Pachter [aut, rev, ths]

concordexR_1.13.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
concordexR/json (API)
NEWS

# Install 'concordexR' in R:
install.packages('concordexR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pachterlab/concordexr/issues

Pkgdown/docs site:https://pachterlab.github.io

On BioConductor:concordexR-1.13.0(bioc 3.24)concordexR-1.12.0(bioc 3.23)

singlecellclusteringspatialtranscriptomics

6.04 score 14 stars 13 scripts 294 downloads 2 exports 73 dependencies

Last updated from:3b93bdfd7a. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE258
linux-devel-x86_64WARNING503
source / vignettesOK389
linux-release-x86_64WARNING453
macos-release-arm64WARNING204
macos-oldrel-arm64WARNING216
windows-develWARNING445
windows-releaseWARNING379
windows-oldrelWARNING396
wasm-releaseOK229

Exports:calculateConcordexrunConcordex

Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelbitbit64blobblustercachemcliclustercodetoolscpp11curlDBIdbplyrDelayedArraydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluehttr2igraphIRangeslambda.rlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpurrrR6rappdirsRcpprjsonrlangRSQLiteS4ArraysS4VectorsSeqinfoSingleCellExperimentsnowSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVector

Using concordex in to assess cluster boundaries in scRNA-seq

Lambda Moses, Kayla Jackson

Rendered fromconcordex-nonspatial.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-06-12
Started: 2024-07-22

Overview of concordexR

Lambda Moses, Kayla Jackson

Rendered fromoverview.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2024-07-22
Started: 2023-03-31

Readme and manuals

Help Manual

Help pageTopics
Identify Spatially Homogeneous Regions with concordexcalculateConcordex calculateConcordex,ANY-method calculateConcordex,SingleCellExperiment-method calculateConcordex,SpatialExperiment-method calculateConcordex,SummarizedExperiment-method runConcordex runConcordex,SingleCellExperiment-method runConcordex,SpatialExperiment-method