This repository contains the source data and source codes for bioinformatic analysis. The paper was published in Nature. 544, 250–254.
| File Name | Description |
|---|---|
| data | source data for the bioinformatic analysis |
| ClonogenicAssay | quantification of circulating tumor cells |
| LungMetQuantify | MATLAB source code for lung macro-metastasis quantification |
| VesselQuantify | CellProfiler pipelines for vessel density/length and co-localization quantifications |
| SUM_PCA | compare ∑GPAGs − ∑PPAGs with the first principle component from Principle Component Analysis (Supplementary Table 1c-f) |
| REVIGO_Plot | source codes for summarizing GPAGs and PPAGs using REVIGO plots (Supplementary Table 2) |
| IF_Visualization | source codes of dot plots for immuno-staining data visualization |
| Immune_Profiling | flow panel design for the immune profiling |
| Fig1 | source codes for Fig. 1a,b,f, and Supplementary Table 1a,b and Supplementary Table 3 |
| Fig4 | source codes for Fig. 4a,b,i,j |
| ExtendedFig1 | source codes for Extended Data Fig. 1b-e |
| ExtendedFig3 | source codes for Extended Data Fig. 3q |
| ExtendedFig7 | source codes for Extended Data Fig. 7b-h |
| ExtendedFig8 | source codes for Extended Data Fig. 8c,d |
You can use git command tool to clone the whole repository.
git clone https://github.com/lintian0616/vesselNormalization.git
Alternatively, you can click Download ZIP and later unzip the file in your local computer.
Should you have any question, please do not hesitate to contact Lin Tian (lintian0616@gmail.com) and cc to Dr. Xiang Zhang (xiangz@bcm.edu).
We thank the following bioinformatic resources for their support on our research.
- CyVerse provides us with computational systems for bioinformatic analysis. All the R programming codes were run on the instance called Data Mining for Cancer Biology.
- GenePattern allows us perform all the Gene Set Enrichment Analysis (GSEA) and single sample GSEA projection (ssGSEA).
- GenomeSpace helps us organize our biological data.
- GitHub and Bitbucket helps us organize our source codes.