| --- |
| tags: |
| - biology |
| - genomics |
| - gene-expression |
| --- |
| |
| # EPInformer pipeline checkpoints |
|
|
| This repository provides the 12-fold leave-chromosome-out checkpoints for the |
| EPInformer pipeline. |
|
|
| ## Gene-expression checkpoints |
|
|
| The `expression_models/` directory contains one checkpoint for each of the |
| 12 leave-chromosome-out folds. `f1` uses distance only, `f2` uses distance and |
| activity, and `f3` uses distance, activity, Hi-C contact, and promoter signal. |
| Each feature configuration is in its own `f1/`, `f2/`, or `f3/` subdirectory. |
|
|
| | Cell type | Assay | f1 | f2 | f3 | |
| |---|---|---:|---:|---:| |
| | K562 | RNA | 0.7528 | 0.8552 | 0.8564 | |
| | K562 | CAGE | 0.8114 | 0.8709 | 0.8673 | |
| | GM12878 | RNA | 0.7610 | 0.8268 | 0.8602 | |
| | GM12878 | CAGE | 0.8270 | 0.8687 | 0.8902 | |
| | H1 | RNA | 0.6608 | 0.7800 | 0.7811 | |
| | HepG2 | RNA | 0.6340 | 0.8382 | 0.8447 | |
| | HUVEC | RNA | 0.6304 | 0.8269 | 0.8390 | |
| | NHEK | RNA | 0.6053 | 0.8177 | 0.8281 | |
|
|
| Values are pooled Pearson R. Use the matching encoder checkpoints, HDF5 input, |
| expression labels, and fold split described in the |
| [EPInformer pipeline README](https://github.com/pinellolab/EPInformer/tree/pipeline). |
|
|
