ChIP-Atlas is the database of the processed data and analysis results of the public ChIP-Seq/DNase-Seq data archived in Sequence Read Archive (SRA). It also provides online data analysis function based on ChIP-Atlas's peak-call database. This repository contains the code of the web application and the documentation of the database.
ChIP-Atlas is providing its full features on chip-atlas.org.
ChIP-Atlas is providing online enrichment analysis feature on ChIP-Atlas - in silico ChIP. The feature is based on the NIG supercomputer system, hosted by DNA Data Bank of Japan, National Institute of Genetics. The feature depends on the computational resources provided by this shared computing cluster while the web application itself is running on the cloud, thus in silico ChIP may go down during the maintenance of the platform.
Processed data including the peak-call data in bed, bigBed or bigWig format is available to download via web application interface (example). We also offer the bulk download of the data via LSDB Archive. We provide individual data for each experiment and data assembled by the curated metadata. See more details about downloading data in Wiki.
Each individual data entry has its sequencing quality data imported from Quanto project, which calculated sequencing quality of data submitted to Sequence Read Archive by FastQC.
The ChIP-Atlas paper is now available on bioRxiv. You can also cite our database via the doi assigned to the data deposited in the National Bioscience Database Center.
- Preprint
- Shinya Oki, Tazro Ohta, et al. Integrative analysis of transcription factor occupancy at enhancers and disease risk loci in noncoding genomic regions. bioRxiv 262899; doi: https://doi.org/10.1101/262899
- Website
- Oki, S; Ohta, T (2015): ChIP-Atlas. http://chip-atlas.org
- Database
- Oki, S; Ohta, T (2015): ChIP-Atlas. http://dx.doi.org/10.18908/lsdba.nbdc01558-000
- Shinya Oki, Kyushu University
- Metadata curation
- Workflow management and execution
- Tazro Ohta, Database Center for Life Science (DBCLS)
- Development/Maintenance of web application
- Development of data model
- Osamu Ogasawara, DNA Data Bank of Japan (DDBJ)
- Support in silico ChIP implementation over NIG supercomputer system
- Hideki Hatanaka, National Bioscience Database Center (NBDC)
- Support data archive on LSDB Archive
See LICENSE.txt for details of copyright of code provided under this repository. Copyright for the data can be browsed at the LSDB Archive website here.