-
Notifications
You must be signed in to change notification settings - Fork 6
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'master' of https://github.com/AllenInstitute/mfishtools
- Loading branch information
Showing
1 changed file
with
2 additions
and
2 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -15,10 +15,10 @@ devtools::install_github("AllenInstitute/mfishtools", build_opts = c("--no-resav | |
|
||
## Library use cases | ||
|
||
There are two primary use cases for this libary, both of which will soon have associated vignettes. | ||
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.** 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. | ||
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 [email protected]. | ||
|
||
|