SPOTlight
Spatial Transcriptomics Capture Location Deconvolution
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
2 of 6 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.4%) to scientific vocabulary
Keywords from Contributors
Repository
Spatial Transcriptomics Capture Location Deconvolution
Basic Info
- Host: GitHub
- Owner: MarcElosua
- License: gpl-3.0
- Language: R
- Default Branch: devel
- Homepage: https://marcelosua.github.io/SPOTlight
- Size: 222 MB
Statistics
- Stars: 189
- Watchers: 2
- Forks: 25
- Open Issues: 12
- Releases: 1
Metadata Files
README.md
Welcome to SPOTlight 
Current build status
- release 
- development 
We are currently on the process of submitting SPOTlight to bioconductor and there have been some styling changes on this branch compared to previous releases. If you want to use the version we are currently submitting feel free to look at the updated vignette here. If you want to keep using the previous versions, you can still find it in the spotlight-0.1.7 branch and follow the previous vignette.
SPOTlight provides a tool that enables the deconvolution of mixtures of cells from a single-cell reference. Originally developed for 10X's Visium - spatial transcriptomics- technology, it can be used for all technologies that output mixtures of cells. It is compatible with Bioconductor's SingleCellExperiment and SpatialExperiment classes as well as dense and sparse matrices. Furthermore, the package also provides visualization tools to assess the results of the deconvolution. Briefly, SPOTlight is based on finding topic profile signatures, by means of an NMFreg model, for each cell type and then optimizing the cell types proportions to fit the mixture we want to deconvolute.
Installation
``` r install.packages("BiocManager") BiocManager::install("SPOTlight")
Or the devel version
BiocManager::install("SPOTlight", version = "devel") ```
Alternatively, you can install it from GitHub using the devtools package.
r
install.packages("devtools")
library(devtools)
install_github("https://github.com/MarcElosua/SPOTlight")
References
- Elosua-Bayes M, Nieto P, Mereu E, Gut I, Heyn H (2021): SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes. Nucleic Acids Res 49(9):e50. doi:10.1093/nar/gkab043.
Contributors
SPOTlight was originally developed by Marc Elosua Bayes and has received substantial additional contributions from Helena L. Crowell.
Issues - Ideas?
SPOTlight is still under active development. We greatly welcome (and highly encourage!) all feedback, bug reports and suggestions for improvement here. Please make sure to raise issues with a reproducible example and the output of your sessionInfo().
Owner
- Name: Marc Elosua Bayés
- Login: MarcElosua
- Kind: user
- Location: Barcelona
- Company: CNAG-CRG
- Twitter: elosua_bayes
- Repositories: 2
- Profile: https://github.com/MarcElosua
🛶
GitHub Events
Total
- Issues event: 5
- Watch event: 25
- Issue comment event: 3
- Push event: 2
- Create event: 1
Last Year
- Issues event: 5
- Watch event: 25
- Issue comment event: 3
- Push event: 2
- Create event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| MarcElosua | e****c@g****m | 446 |
| HelenaLC | h****a@c****u | 13 |
| Federico Marini | m****f@u****e | 4 |
| Nitesh Turaga | n****a@g****m | 2 |
| J Wokaty | j****y@s****u | 2 |
| J Wokaty | j****y | 2 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 3
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Total downloads:
- bioconductor 15,042 total
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 10
- Total maintainers: 1
proxy.golang.org: github.com/marcelosua/spotlight
- Documentation: https://pkg.go.dev/github.com/marcelosua/spotlight#section-documentation
- License: gpl-3.0
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Latest release: v0.1.0
published about 6 years ago
Rankings
proxy.golang.org: github.com/MarcElosua/SPOTlight
- Documentation: https://pkg.go.dev/github.com/MarcElosua/SPOTlight#section-documentation
- License: gpl-3.0
-
Latest release: v0.1.0
published about 6 years ago
Rankings
bioconductor.org: SPOTlight
`SPOTlight`: Spatial Transcriptomics Deconvolution
- Homepage: https://github.com/MarcElosua/SPOTlight
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/SPOTlight/inst/doc/SPOTlight.pdf
- License: GPL-3
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Latest release: 1.12.1
published 12 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.1 depends
- Matrix * imports
- NMF * imports
- SingleCellExperiment * imports
- ggplot2 * imports
- matrixStats * imports
- nnls * imports
- stats * imports
- BiocStyle * suggests
- DelayedArray * suggests
- ExperimentHub * suggests
- S4Vectors * suggests
- Seurat * suggests
- SeuratObject * suggests
- SpatialExperiment * suggests
- SummarizedExperiment * suggests
- TENxVisiumData * suggests
- TabulaMurisSenisData * suggests
- colorBlindness * suggests
- ggcorrplot * suggests
- grDevices * suggests
- grid * suggests
- igraph * suggests
- jpeg * suggests
- knitr * suggests
- methods * suggests
- png * suggests
- rmarkdown * suggests
- scater * suggests
- scatterpie * suggests
- scran * suggests
- testthat * suggests