concordexR
Identify Spatial Homogeneous Regions with concordex
Bioconductor version: 3.23 · Package version: 1.12.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("concordexR")Details
| Maintainer | Kayla Jackson <kaylajac@caltech.edu> |
| Author | Kayla Jackson [aut, cre] (ORCID: <https://orcid.org/0000-0001-6483-0108>), A. Sina Booeshaghi [aut] (ORCID: <https://orcid.org/0000-0002-6442-4502>), Angel Galvez-Merchan [aut] (ORCID: <https://orcid.org/0000-0001-7420-8697>), Lambda Moses [aut] (ORCID: <https://orcid.org/0000-0002-7092-9427>), Alexandra Kim [ctb], Laura Luebbert [ctb] (ORCID: <https://orcid.org/0000-0003-1379-2927>), Lior Pachter [aut, rev, ths] (ORCID: <https://orcid.org/0000-0002-9164-6231>) |
| License | Artistic-2.0 |
| URL | https://github.com/pachterlab/concordexR, https://pachterlab.github.io/concordexR/ |
| Bug Reports | https://github.com/pachterlab/concordexR/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, SingleCell, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/concordexR/ |
Citation
From within R, enter citation("concordexR"):
Kayla Jackson, A. Sina Booeshaghi, Angel Galvez-Merchan, Lambda Moses, Lior Pachter. concordexR: Identify Spatial Homogeneous Regions with concordex. doi:10.18129/B9.bioc.concordexR, R package version 1.12.0, https://bioconductor.org/packages/concordexR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | concordexR_1.12.0.tar.gz |
| Windows binary (x86_64) | concordexR_1.12.0.zip |
| macOS binary (arm64) | concordexR_1.12.0.tgz |
| macOS binary (x86_64) | concordexR_1.12.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: BiocGenerics, BiocNeighbors, BiocParallel, bluster, cli, DelayedArray, Matrix, methods, purrr, rlang, SingleCellExperiment, sparseMatrixStats, SpatialExperiment, SummarizedExperiment
Suggests: BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans, patchwork, rmarkdown, scater, SFEData, SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0)