From 923c80fa1c2ef93c0b40cadc32bb2ca99bdc98cf Mon Sep 17 00:00:00 2001 From: Jeremy Miller Date: Thu, 3 Jan 2019 11:00:21 -0800 Subject: [PATCH] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index beecc07..5464881 100644 --- a/README.md +++ b/README.md @@ -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 jeremym@alleninstitute.org.