concordexR
Compute the neighborhood consolidation matrix and identify SHRs
Science Score: 59.0%
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Found 5 DOI reference(s) in README -
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Low similarity (14.4%) to scientific vocabulary
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Repository
Compute the neighborhood consolidation matrix and identify SHRs
Basic Info
- Host: GitHub
- Owner: pachterlab
- License: artistic-2.0
- Language: R
- Default Branch: main
- Homepage: https://pachterlab.github.io/concordexR/
- Size: 13 MB
Statistics
- Stars: 13
- Watchers: 4
- Forks: 0
- Open Issues: 1
- Releases: 0
Created almost 3 years ago
· Last pushed 9 months ago
Metadata Files
Readme
Changelog
License
README.Rmd
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "70%"
)
```
# concordexR
[](https://codecov.io/gh/pachterlab/concordexR)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/concordexR)
The goal of concordexR is to identify spatial homogeneous regions (SHRs) as
defined in the recent manuscript, ["Identification of spatial homogenous regions in tissues with concordex"](https://doi.org/10.1101/2023.06.28.546949). Briefly, SHRs are are
domains that are homogeneous with respect to cell type composition. `concordex`
relies on the the k-nearest-neighbor (kNN) graph to representing similarities
between cells and uses common clustering algorithms to identify SHRs.
## Installation
Versions of the `concordexR` package that do not enable clustering spatial data
into spatial homogeneous regions (SHRs) are available for Bioconductor versions
3.17-19. The most recent version of the package is slated to be released on
Bioconductor version 3.20.
```{r}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version="3.20")
BiocManager::install("concordexR")
```
## Example
This is a basic example using concordex:
```{r load libraries}
library(SFEData)
library(Voyager)
library(scran)
library(bluster)
library(concordexR)
```
```{r}
sfe <- McKellarMuscleData("small")
clusters <- quickCluster(sfe, min.size=2, d=15)
```
```{r example}
nbc <- calculateConcordex(
sfe,
clusters,
n_neighbors=10,
BLUSPARAM=KmeansParam(2)
)
colData(sfe)[["shr"]] <- attr(nbc, "shrs")
```
```{r plot-shr}
plotSpatialFeature(sfe, features="shr")
```
## Citation
If you'd like to use the `concordexR` package in your research, please cite our
recent bioRxiv preprint
> Jackson, K.; Booeshaghi, A. S.; Gálvez-Merchán, Á.; Moses, L.; Chari, T.; Pachter, L. Quantitative assessment of single-cell RNA-seq clustering with CONCORDEX. bioRxiv (Cold Spring Harbor Laboratory) 2023. https://doi.org/10.1101/2023.06.28.546949.
> @article {Jackson2023.06.28.546949,
author = {Jackson, Kayla C. and Booeshaghi, A. Sina and G{\'a}lvez-Merch{\'a}n, {\'A}ngel and Moses, Lambda and Chari, Tara and Kim, Alexandra and Pachter, Lior},
title = {Identification of spatial homogeneous regions in tissues with concordex},
year = {2024},
doi = {10.1101/2023.06.28.546949},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2024/07/18/2023.06.28.546949},
journal = {bioRxiv}
}
## Maintainer
[Kayla Jackson](https://github.com/kayla-jackson)
Owner
- Name: Pachter Lab
- Login: pachterlab
- Kind: organization
- Email: lpachter@caltech.edu
- Location: Pasadena, CA
- Website: http://pachterlab.github.io
- Repositories: 128
- Profile: https://github.com/pachterlab
GitHub Events
Total
- Issues event: 1
- Watch event: 3
- Issue comment event: 1
- Push event: 15
Last Year
- Issues event: 1
- Watch event: 3
- Issue comment event: 1
- Push event: 15
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Kayla Jackson | k****c@c****u | 196 |
| Lambda Moses | d****2@c****u | 13 |
| J Wokaty | j****y | 8 |
| Kayla Jackson | k****n@K****l | 2 |
| A Wokaty | a****y@s****u | 2 |
Committer Domains (Top 20 + Academic)
caltech.edu: 2
sph.cuny.edu: 1
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 4
- Total pull requests: 1
- Average time to close issues: 16 days
- Average time to close pull requests: 11 minutes
- Total issue authors: 4
- Total pull request authors: 1
- Average comments per issue: 1.25
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 0
- Average time to close issues: 16 days
- Average time to close pull requests: N/A
- Issue authors: 4
- Pull request authors: 0
- Average comments per issue: 1.25
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- LTLA (1)
- alecbarrett (1)
- ynanli (1)
- HelenaLC (1)
Pull Request Authors
- lambdamoses (1)
Top Labels
Issue Labels
bug (1)
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 5,525 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: concordexR
Identify Spatial Homogeneous Regions with concordex
- Homepage: https://github.com/pachterlab/concordexR https://pachterlab.github.io/concordexR/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/concordexR/inst/doc/concordexR.pdf
- License: Artistic-2.0
-
Latest release: 1.8.0
published 10 months ago
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 31.5%
Downloads: 94.4%
Maintainers (1)
Last synced:
6 months ago