EpiDiP Server  Epigenomic Digital Pathology

Compatibility options / Mirror sites

Mirror 1 - MAIN

Collects all uploads from all sites; fastest hardware setup. We suggest using this mirror.
https://epidip.usb.ch with SSL, with GPU acceleration
http://epidip.usb.ch without SSL, with GPU

Mirror 2 - BACKUP

Only contains IDATs uploaded here and most data before Sept. 2023.
https://www.epidip.org with SSL, without GPU
http://www.epidip.org without SSL, without GPU

Mirror 3 - 450K/EPIC v1 - previous version

You can still use the 450K/EPIC v1 page. Note that IDAT files uploaded to one of the sites, i.e. legacy, .org, .usb.ch, are currently synchronized to the .usb.ch site, which runs on the fastest hardware.

Please report errors / bugs to juergen.hench@usb.ch, preferably indicating date and time of the error and the URL that was used. If allowed, please indicate one of the affected Sentrix IDs as well.

Upload IDAT methylation array datasets

IDAT uploader (Human Methylation 450K, EPIC v1 850K, EPIC v2 950K*)

View methylome UMAP plot

UMAP plot viewer
UMAP plot refreshes approx. every hour (GPU) or every 3 to 4 hours irrespective of individual uploads. Please allow this time before your uploaded files can be visualized. Depending on your internet connection, you may need to try which of our mirror sites works best for you. The two mirrors (.org / usb.ch) are currently not synchronized with regard to case uploads, but this is planned in the near future. Hence, your uploaded case will only appear on the mirror(s) you have used for uploading the IDAT files.

*) EPIC v2 note: We suggest restricting to 25K probes.

View copy number profiles

Click on respective dot in the UMAP plots to open copy number profiles of individual cases.

UMAP coordinates

Download UMAP plot as coordinates as XLSX spreadsheets

Reference annotations:

Pan-cancer annotation: 
1gqhMju0tGls9kt2LAj67kRgO9kMtWE2YQTtP6W-K6Xc
Brain tumor annotation (from GSE90496): 
1VdwYNBgWbqMmzTGpIk3xkoAoowQeOPQ3Q-Yee9L_06o
Soft tissue tumor annotation (from GSE140686): 
1ZisC74J7LHouoYND3B8vdAeB8aMbCmiZBawypAyHd-I

Nanopore epigenetic and copy number analysis  NanoDiP

Nanopore Digital Pathology: For legal reasons, nanopore raw data must not be analyzed on our public server. However, this is established through a different tool. The NanoDiP tool is illustrated under: NanoDiP demonstration page
You can analyze your own data with a local copy of the virtual machine: NanoDiP demonstration virtual machine (VirtualBox OVA, large file!)
Alternatively, you can build NanoDiP from source (reference data not included): NanoDiP source code

General information & manuals

This is the web portal for epigenomic diagnostics within the Dept. of Neuropathology, Institute for Medical Genetics and Pathology, University Hospital Basel, Switzerland. EpiDiP stands for Epigenomic Digital Pathology and deals with the visualization and cross-comparison of (microarray-based) methylome datasets. From here, you can launch our web applications. Usage is free of charge but comes without warranty.

EpiDiP User Manual
Methylation Class Descriptions (Annotation)
Methodology article describing this platform: https://actaneurocomms.biomedcentral.com/articles/10.1186/s40478-024-01759-2
last update: 2024-04-04, University Hospital Basel, Pathology