This is a public repository for the code associated to the paper: Czarnewski et al (2019) Nat Communications.
The analysis done within the paper was divided in serveral summary reports as follows. The files were generated after the initial analysis, which depend on random number for i.e. the tSNE and other functions. Seeds were added to those now. Thus some slight differences in the plots can be observed. However, the conclusions and interpretations are the same.
| notebook | Reference | GEO | figure |
|---|---|---|---|
| mouse_colitis | This paper | GSE131032 | Fig 2a-c, S3, S4 |
| mouse_colitis_vs_UC | Taman et al (2018) J Crohns Colitis | ---- | Fig 2d-e |
| mapping_ibd_risk_genes | Huang et al (2017) Nature | ---- | Fig S5 |
| uc_classification_microarray | Arijs et al (2009) Gut Arijs et al (2009) Plos One Toedter et al (2018) Am J Gastroenterol Arijs et al (2016) Gut |
GSE12251 GSE16879 GSE23597 GSE73661 |
Fig 1, 3, 4, 5, S1, S6, S7, S8 |
| uc_classification_rnaseq | Haberman et al (2019) Nat Communications | GSE109142 | Fig 5, S8, S9 |
If you are interested also in the raw .Rmd files, please check the scripts folder.