Help index
CCSI is an integrated database for the collection, interpretation and analysis of chromatin interaction data. It contains 91 sets of chromosomal 3D (three-dimensional) data collected from published literature, UCSC database and NCBI GEO database, resulting in a total of 3,017,962 pairwise interactions. The search engine is the most remarkable feature for information acquisition. All involved data along with analysis pipeline are released for download.
1). Search page
2). Search result
With regard to hidden features, clicking 'plus' button will give details.
Browser page (Browser is fast for mm10, while a bit slow for hg38 owing to its larger genome size.)
1). Part1-1: Interaction pairs with annotation
The source and description about each dataset refer to the right columns. Click the filename, user can download complete interaction datasets with annotation. Take “3c-1” for example,Part1-2: Interaction pairs without annotation
Similar to part1-1, they are interaction datasets without annotation.2). Part2: Genome annotation file, enhancer positions and SNPs
Click the filename for download.3). Part3: Analysis pipeline
To run the "pipeline.py", user just need to prepare config file and input files, and "readme" file provides the detailed instruction.