Clump sequencing exposes the spatial expression programs of intestinal secretory cells

Code and input data for Clump-Seq: spatial reconstruction for goblet, tuft and enteroendocrine cells 
This is a collection of input data files and analysis scripts which were used in our manuscript "Clump sequencing exposes the spatial expression programs of intestinal secretory cells".
Prerequisites
* Matlab R2019_a
Scripts
* clumps_assign_zone – assigns a zone along the crypt to villus axis  to each clump
* clumps_geometrical_classification_per_n – classifies clumps according to their content of secretory cells, separately for pairs and larger clumps
* clumps_n_unify_visualize – merges data for pairs and larger clumps
* clumps_seperate_by_secretory_type – creates a separate struct for clumps containing each of the secretory cell types: goblet, tuft and EE cells
* goblet_SC_reconstruction – zonation reconstruction for single goblet cells based on clumps derived land marks
* tuft_SC_reconstruction– zonation reconstruction for single tuft cells based on clumps derived land marks
* EE_SC_reconstruction– zonation reconstruction for single enteroendocrine cells based on clumps derived land marks
* MATLAB supporting functions – folder containing all functions called by these scripts
Input files
* clumps_struct.mat – SC RNA seq results for clumps. Fields:
* entero_SC_zonation_struct.mat – zonation reconstruction for single enterocytes as performed in the paper “Spatial Reconstruction of Single Enterocytes Uncovers Broad Zonation along the Intestinal Villus Axis” by Moor et. Al , Cell ,2018.
* rita_keren_epi_MARS_seq_combined_gob.mat - SC RNA seq for single goblet cells. Fields: view details for clumps_struct.mat. Data source: experiments performed by manuscript authors.
* EE_clevers.mat - SC RNA seq for single enteroendocrine cells. Fields: view details for clumps_struct.mat, additional fields refer to temporal data not used for zonation reconstruction. Data source: GEO: GSE113561
* tuft_our_atlas.mat - SC RNA seq for single tuft cells. Fields: view details for clumps_struct.mat