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This folder contains GenoSTAN chromatin state annotations for 127 cell types and tissues (genome version hg20/hg38 (GRCh38)) from Zacher et al. (2016). Chromatin state annotations are available for GenoSTAN-Poilog and GenoSTAN-nb as bed files or GRanges objects objects (for compatibility with Bioconductor). Signal (whole genome) and training data (ENCODE pilot regions [except dataset1]) are available as R data files. External data used for benchmarking of the segmentations are also available for download as Granges objects.
The summarized annotation (GenoSTAN-Poilog) for promoters and enhancers is available in files GenoSTAN_enhancers.bed/GenoSTAN_enhancers.rda and GenoSTAN_promoters.bed/GenoSTAN_promoters.rda.
Cell types and tissuesare labeled using the Epigenome ID (EID) from the Roadmap Epigenomics project. A mapping of EID to a description of the cell type, tissue and sample type can be found in EID_annotation.tab.
To download all files type: wget -rc http://i12g-gagneurweb.in.tum.de/public/paper/GenoSTAN
| Name | Last modified | Size | Description |
|---|---|---|---|---|
| Parent Directory | - | ||
| chromatin_state_annotations/ | 2016-02-22 13:17 | - | |
| external_data/ | 2023-03-29 10:50 | - | |
| signal_files/ | 2016-06-30 10:30 | - | |
| training_data/ | 2016-06-30 10:37 | - | |
| EID_annotation.tab | 2016-02-22 11:05 | 8.5K | |
| GenoSTAN_enhancers.bed.gz | 2016-02-22 11:07 | 18M | |
| GenoSTAN_enhancers.rda | 2016-02-22 11:07 | 12M | |
| GenoSTAN_promoters.bed.gz | 2016-02-22 11:53 | 12M | |
| GenoSTAN_promoters.rda | 2016-02-22 11:53 | 7.6M | |
| README | 2016-06-30 10:44 | 937 | |