This code repository contains all code needed to reproduce the results in "High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamics".
Here's a graphical overview of our main findings from this paper:
To learn more about this project, click on this link to access our manuscript
To reproduce the results, start at the Protocol RMD file, then move through the figure files. Note that the MD files provide a more readable representation of these RMD files if you're interested in looking through the code but not running it.
- Protocol_Revisions.Rmd makes the files we use to generate the graphs in the figure files.
- Protocol_Revisions.md is the corresponding human readable version
- Figure1_Revisions.Rmd makes the figures contained in Figure 1 of the paper.
- Figure1_Revisions.md is the corresponding human readable version
- Figure2_Revisions.Rmd makes the figures contained in Figure 2 of the paper.
- Figure2_Revisions.md is the corresponding human readable version
- Figure3_Revisions.Rmd makes the figures contained in Figure 3 of the paper.
- Figure3_Revisions.md is the corresponding human readable version
- Figure4_Revisions.Rmd makes the figures contained in Figure 4 of the paper.
- Figure4_Revisions.md is the corresponding human readable version
- Figure5_Revisions.Rmd makes the figures contained in Figure 5 of the paper.
- Figure5_Revisions.md is the corresponding human readable version
- Supplement_Revisions.Rmd makes the figures contained in the Supplemental Figures of the paper.
- Supplement_Revisions.md is the corresponding human readable version
To easily see which code generates which graphs without running anything, check out the .md files (e.g. Figure4_Revisions.md).