Data processing and analysis scripts for our spatial profiling of mouse embryos using seqFISH as described in https://www.biorxiv.org/content/10.1101/2020.11.20.391896v1
scripts: Scripts can be found in the scripts folder, with a description and order of running in script_descriptions.txt
functions: R code containing functions required for running scripts.
SpatialMouseAtlas: Code for the Shiny app can be found in the SpatialMouseAtlas folder. Note that the data folder within the app can be downloaded from the Data link (below).
Processed Data Download: is available to download here https://content.cruk.cam.ac.uk/jmlab/SpatialMouseAtlas2020/
Shiny app: Interactive visualisation here https://marionilab.cruk.cam.ac.uk/SpatialMouseAtlas/
Gene expression imputation, midbrain-hindbrain boundary selection, and independent smFISH processing: Scripts are available here https://github.com/MarioniLab/amScripts_mouseEmbryoFISH
Contact: shila.ghazanfar - at - cruk.cam.ac.uk or marioni - at - ebi.ac.uk