Published September 1, 2025 | Version v2
Dataset Open

Single-cell and spatial transcriptomics of stricturing Crohn's disease

Authors/Creators

Contributors

Contact person:

  • 1. ROR icon Massachusetts General Hospital
  • 2. ROR icon Harvard Medical School
  • 3. ROR icon Broad Institute

Description

This folder contains the spatial transcriptomics data + code. This code was generated by members of the Smillie Lab @ MGH and Harvard Medical School.

  • github.tar.gz: spatial analysis code and data
  • anndata.h5ad: anndata object (scanpy)
  • V*tar.gz: raw spatial transcriptomics files

The github.tar.gz folder contains everything you need to reproduce the spatial transcriptomics figures. It is structured as follows:

  • 1.BayesPrism: code for running BayesPrism on spatial data
  • 2.SparCC: code for running SparCC on spatial data
  • 3.Lasso: code for running lasso regression on spatial data
  • 4.Analysis: code for reproducing all figures in the paper
  • 4.Analysis/1.analysis.r: script to reproduce all figures in the paper ***
  • code: code library containing all necessary functions
  • load_data.r: code to load the single-cell and spatial datasets
  • sco.rds: single-cell analysis object (10X Chromium) formatted as an R list
  • vis.rds: spatial analysis object (10X Visium) formatted as an R list

All scripts are numbered. You need to run everything in order. For convenience, we include the output files for 1.BayesPrism, 2.SparCC, and 3.Lasso, allowing you to skip straight to the analysis code in 4.Analysis.

To reproduce all figures in the paper, you need to do the following:

  1. Edit your PROJECT_FOLDER in the header of load_data.r
  2. Install the packages listed at the top of load_data.r
  3. Go to the 4.Analysis directory, start an interactive R session, and type:
    > source('1.analysis.r')

This will load the beginning of the 1.analysis.r script (until the stop() statement on line 68). You can run the code in two different ways:

  1. You can step through the code line by line in your interactive R session (starting at line 68)
  2. Alternatively, remove the stop() statement from the script, then run the code start to finish

If you encounter any errors, try to debug them using a combination of Google+ChatGPT. If you still have trouble, please contact the Smillie Lab.

Note: the single-cell and spatial code are also available on GitHub. However, the spatial analysis requires large files that cannot be hosted on GitHub. Therefore, it is better to download the code + files from Zenodo. The GitHub link is provided below:

https://github.com/LJ-Kong/fibrosis_scRNA_stRNA

 

 

 

 

Files

Files (8.7 GB)

Name Size
md5:69eb5a9b026dff5cfb63641c6c4058a6
2.2 GB Download
md5:3191c4f2e247d22d4e40db19abbc0d1b
5.9 GB Download
md5:7aed52f8f9633ead8e90d66eabd72165
42.7 MB Download
md5:b671f6847d02ef68c8b8ece264748082
30.7 MB Download
md5:34040bd938305e14ae1199056c89aef9
26.8 MB Download
md5:12f86dd2bd883ac9850d236c22240a27
57.2 MB Download
md5:dafbb92d463c8dd03add18b06a7bc341
42.3 MB Download
md5:45c5be5846d9209a4cf4d9a80e28b7a1
22.7 MB Download
md5:0910a94c18b979bf954dc8ab9000d0c5
25.9 MB Download
md5:35e0f412d3d1931c0386fb6631b4988d
34.3 MB Download
md5:2b078d937287a9bc030851337ba840f1
36.6 MB Download
md5:1edad7e5bed6e379cccd9d901aa14e9d
14.4 MB Download
md5:4b96fcddbe5a30db46baebaa856b2a52
18.6 MB Download
md5:e1269d371536e32bfaf0bfec36dbf720
30.5 MB Download
md5:27e42180d9ef204d27602835a3588582
29.2 MB Download
md5:353a0ab1bb1a4443632ad4d431322805
32.3 MB Download
md5:5c871c1875d703cd9d65f6a482baefa6
29.2 MB Download
md5:c33c2197c2ccb70ca26620e31ebf2dc0
34.4 MB Download
md5:59981034b717ff177568d7369d140dbe
30.9 MB Download
md5:5465a2b0f5de28b74a6103996ee999a1
25.3 MB Download
md5:43486d8837af8175580b4d1474434f56
19.0 MB Download
md5:56a1d1f7060adcbdc7c419c0108521b0
36.6 MB Download

Additional details

Software

Repository URL
https://github.com/LJ-Kong/fibrosis_scRNA_stRNA
Programming language
R , Python