https://github.com/bigpaul97/ccle
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
-
✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (8.0%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bigpaul97
- Language: MATLAB
- Default Branch: main
- Size: 4.24 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Conserved-current loop extrusion (CCLE)
This repository contains all the necessary codes for running the CCLE simulation, carrying out experiment-simulation Hi-C comparison, and calculating various metrics for goodness-of-fit.
To cite the code: 
CCLE_main:
This folder comprehensively contains the codes for the CCLE simulation program. The main code for running the simulation is named "CCLE_main.m".
The only input file is the file of ChIP-seq data of the protein of interest.
The most important output of the program are (1) the simulated Hi-C map, named "hmap", (2) the simulated loop anchor positions, named "lsitestraj" (for left anchors) and "rsitestraj" (for right anchors), and (3) time series, named "ts_traj".
Please refer to the comments in the "CCLE_main.m" file for more details about parameter adjustment or explanation.
This folder also contains subfolders with the yeast ChIP-seq data used in the paper.
HiCcompareexp_sim:
This folder contains the codes that generate Hi-C map comparison between the experimental and the simulated Hi-C.
The main code to run is named "HiCcompareexp_sim.m".
Please read the comments in the main code file for more instructions.
HiCcompareexp_exp:
This folder contains the codes that generate Hi-C map comparison between two experimental Hi-C maps.
The main code to run is named "HiCcompareexp_exp.m".
Please read the comments in the main code file for more instructions.
ChIP-seq_correlation:
This folder contains the program that generates the ChIP-seq correlation plots.
Please read to the comments in the file "chipseq_correlation" for more instructions.
Hi-C expeiments:
This folder contains a few examples of the experimental Hi-C maps used in the paper.
These example experimental Hi-C can be used as tests or templates.
Owner
- Login: bigpaul97
- Kind: user
- Repositories: 1
- Profile: https://github.com/bigpaul97