| Database name | Organisms | Data type | Link | Access | Commentaries |
|---|---|---|---|---|---|
| Replication domain | ARABIDOPSIS, Chinese Hamster (C. GRISEUS) , Fruit Fly (D.Megalonaster), Chicken (G. Gallus), Human (Homo sapiens), Mouse (Mus Musculus) , Yeast (S. Pombe) | RT , 4C , GE ,... | https://www2.replicationdomain.com | Open | |
| The genetic architecture of DNA replication timing in human pluripotent stem cells | Human | RT chip-seq histone individual genomes | https://www.nature.com/articles/s41467-021-27115-9 | Data comes from various sources, some with restricted access (genetic ones) |
| Database name | Organisms | Data type | Link | Access | Commentaries |
|---|---|---|---|---|---|
| ENCODE | Human (Homo sapiens), Mouse (Mus Musculus), Caenorhabditis elegans , Fruit Fly (D. Melanogaster) | Histones, TRanscription factors | https://www.encodeproject.org/ | Open | |
| IHEC | Human (Homo sapiens), Mouse (Mus Musculus) | Subset of Histones, Methylome, transcriptome | https://epigenomesportal.ca/ihec/grid.html?assembly=1&build=2020-10 | Open | |
| Roadmap epigenome | Human (Homo sapiens) | Histones, DNase, RNASeq, Methylation | https://egg2.wustl.edu/roadmap/web_portal/index.html | Open | |
| Deep Blue | Human | Histones, chip-seq DNase | https://deepblue.mpi-inf.mpg.de/dashboard.php#ajax/dashboard.php | Open | regroup different databases (Encode, CHIP Atlas, CEEHRC ,Blueprint epigenome, Roadmap epigenomics) Has a programatic acces |
| Yeast Epigenome | Yeast (S. Cerevisae ) | CHip seq exo | http://www.yeastepigenome.org | Open | 400 different targets, bulk download available https://github.com/CEGRcode/2021-Rossi_Nature |
| Chromatin dynamics during DNA replication | Yeast (S. Cerevisae ) | CHip seq | ENA; https://www.ebi.ac.uk/ena/)PRJEB11501, PRJEB13262, and PRJEB11977. | Open |
| Name | Type of models | Input type | Output Type | Main Results | Usability | Reproductibility | Alterable | Data | Commentaries | Link |
|---|---|---|---|---|---|---|---|---|---|---|
| Avocado | Dense NN | assay, cell type, genomic position (positionnal encoding at 25 bp) | value of the experiment at the given position | Creates an embedding for a cell type an assay an all elong the genome | Great (tutorials availabel) | Ok on a smaller training set | Code is clean | Open (from ENCODE) but need to be gathered | I modified the code to use CNN for embedding. (It seems to work well) . There is a preprint that use data in human to improve result on mouse. Could the assay embedding be changed to a protein embedding? | https://github.com/jmschrei/avocado |
| MARS | Graph NN | Single cell transcriptome | cell embedding | Allows to discover and classify celll type | https://github.com/snap-stanford/mars |