https://github.com/alleninstitute/mfishtools
Building Gene Sets and Mapping mFISH Data
https://github.com/alleninstitute/mfishtools
Last synced: 6 months ago
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Building Gene Sets and Mapping mFISH Data
- Host: GitHub
- URL: https://github.com/alleninstitute/mfishtools
- Owner: AllenInstitute
- License: other
- Created: 2018-06-11T23:19:09.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2023-06-08T19:03:58.000Z (about 3 years ago)
- Last Synced: 2025-02-03T14:14:42.495Z (over 1 year ago)
- Language: HTML
- Size: 2.07 MB
- Stars: 16
- Watchers: 4
- Forks: 6
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
*(See a better-formatted version of this page at https://alleninstitute.github.io/mfishtools/)*
# mfishtools
R functions for gene selection and analysis of mFISH data
mfishtools includes many functions that are used for analysis of data for the CZI SpaceTx project, and mostly relies on correlation-based analysis with filtering. *This library is still in beta testing and may be buggy. Community involvement is encouraged through both issues and pull requests.*
## Installation
Install prerequisites:
```
install.packages("devtools")
devtools::install_github("AllenInstitute/scrattch.vis")
devtools::install_github("AllenInstitute/tasic2016data")
```
Note that some people may need to manually install the `GO.db` and `WGCNA` libraries as well:
```
install.packages("BiocManager")
BiocManager::install("GO.db")
BiocManager::install("WGCNA")
```
Install `mfishtools` using:
```
# Quickly, but without the vignettes:
devtools::install_github("AllenInstitute/mfishtools")
# More slowly, but with the vignettes:
install.packages("remotes", repos='http://cran.us.r-project.org')
remotes::install_github("AllenInstitute/mfishtools", build_vignettes = TRUE)
```
## Library use cases
There are two primary use cases for this libary:
1. **Building a combinatorial marker gene panel for spatial transcriptomics.** [LINK TO VIGNETTE](http://htmlpreview.github.io/?https://github.com/AllenInstitute/mfishtools/blob/master/vignettes/inhibitory_marker_selection.html) This allows the generation of computationally "optimal" marker gene panels based on single cell/nucleus RNA-Seq reference data. A starting set of manually-selected marker genes is first selected, and then the remaining genes are chosen using a greedy algorithm. Relevant statistics and plots are generated that show the predicted success for the panel.
2. **Mapping cells from spatial transcriptomics data sets to reference cell types.** [LINK TO VIGNETTE](http://htmlpreview.github.io/?https://github.com/AllenInstitute/mfishtools/blob/master/vignettes/inhibitory_marker_mapping.html) This allows for cell type calling of cells in a spatial transcriptomics study, and also predicts the accuracy of the calls based on reference data. *Note: it is currently unclear how reliable this method is at correctly predicting cell type calls. Please review results carefully!* Plots can also be generated to show the results.
Many functions are currently not included in these vignettes; please use the R help ("?") if additional information is needed, or e-mail me at jeremym@alleninstitute.org.
## License
The license for this package is available on Github at: https://github.com/AllenInstitute/mfishtools/blob/master/LICENSE
## Level of Support
We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests.
## Contribution Agreement
If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in full at: https://github.com/AllenInstitute/mfishtools/blob/master/CONTRIBUTION