concordexR
Identify Spatial Homogeneous Regions with concordex
Bioconductor version: Release (3.20)
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] 
, A. Sina Booeshaghi [aut] , Angel Galvez-Merchan [aut] , Lambda Moses [aut] , Alexandra Kim [ctb], Laura Luebbert [ctb] , Lior Pachter [aut, rev, ths]
Maintainer: Kayla Jackson <kaylajac at caltech.edu>
citation("concordexR")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("concordexR")
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("concordexR")| concordex-nonspatial | HTML | R Script |
| overview | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0) |
| 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 |
See More
| Suggests | BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans, patchwork, rmarkdown, scater, SFEData, SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | concordexR_1.6.0.tar.gz |
| Windows Binary (x86_64) | concordexR_1.6.0.zip |
| macOS Binary (x86_64) | concordexR_1.6.0.tgz |
| macOS Binary (arm64) | concordexR_1.5.6.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/concordexR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/concordexR |
| Bioc Package Browser | https://code.bioconductor.org/browse/concordexR/ |
| Package Short Url | https://bioconductor.org/packages/concordexR/ |
| Package Downloads Report | Download Stats |