smoothclust
Method for segmentation of spatial domains with smooth boundaries and clustering in spatial transcriptomics
Science Score: 36.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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1 of 3 committers (33.3%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (8.2%) to scientific vocabulary
Keywords from Contributors
Repository
Method for segmentation of spatial domains with smooth boundaries and clustering in spatial transcriptomics
Basic Info
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
smoothclust
Overview
smoothclust is a method for segmentation of spatial domains and spatially-aware clustering in spatial transcriptomics data. The method generates spatial domains with smooth boundaries by smoothing gene expression profiles across neighboring spatial locations, followed by unsupervised clustering. Spatial domains consisting of consistent mixtures of cell types may then be further investigated by applying cell type compositional analyses or differential analyses.
Installation
The smoothclust package can be installed from Bioconductor as follows (using R version 4.4 onwards). This is the recommended installation for most users. Additional details are shown on the Bioconductor package landing page.
install.packages("BiocManager")
BiocManager::install("smoothclust")
The latest development version of the package can also be installed from the development version of Bioconductor, or alternatively from GitHub as follows.
remotes::install_github("lmweber/smoothclust")
Tutorial
For a tutorial and example workflow, see the package vignette.
Citation
In preparation.
Owner
- Name: Lukas Weber
- Login: lmweber
- Kind: user
- Location: Boston, MA
- Company: Boston University
- Website: https://lmweber.org/
- Repositories: 75
- Profile: https://github.com/lmweber
Assistant Professor, Department of Biostatistics, Boston University
GitHub Events
Total
- Push event: 9
- Create event: 2
Last Year
- Push event: 9
- Create event: 2
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Lukas Weber | l****u@g****m | 127 |
| J Wokaty | j****y | 4 |
| A Wokaty | a****y@s****u | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
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Packages
- Total packages: 1
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Total downloads:
- bioconductor 3,701 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: smoothclust
smoothclust
- Homepage: https://github.com/lmweber/smoothclust
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/smoothclust/inst/doc/smoothclust.pdf
- License: MIT + file LICENSE
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Latest release: 1.4.0
published about 1 year ago