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concordexR
This is thedevelopment version of concordexR; for the stable release version, seeconcordexR.
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("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 develBiocManager::install(version='devel')BiocManager::install("concordexR")For older versions of R, please refer to the appropriateBioconductor 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 | 1.11.0 |
| 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/concordexRhttps://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
FollowInstallation instructions to use this package in your R session.
| Source Package | concordexR_1.11.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | concordexR_1.11.0.tgz |
| macOS Binary (arm64) | concordexR_1.11.0.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 |