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Building Gene Sets and Mapping mFISH Data
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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.

Install using:

# Quickly, but without the vignettes:

# More slowly, but with the vignettes:
devtools::install_github("AllenInstitute/mfishtools", build_opts = c("--no-resave-data", "--no-manual"))

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 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 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


The license for this package is available on Github at:

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:

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