concordexR
This is the development version of concordexR; for the stable release version, see concordexR.
Identify Spatial Homogeneous Regions with concordex
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.13.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 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 |
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_1.13.0.tar.gz |
| Windows Binary (x86_64) | concordexR_1.13.0.zip |
| macOS Binary (big-sur-x86_64) | concordexR_1.13.0.tgz |
| macOS Binary (sonoma-arm64) | concordexR_1.13.0.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 |