ATLAS-D2K User and Submitter Guide
This is the home of public documentation for the ATLAS-D2K Center, which publishes data and resources from the GUDMAP and ReBuilding A Kidney (RBK) consortiums. If you find anything that needs correcting or have suggestions for more documentation, please send email to:
Accessing the ATLAS-D2K Data
- Data Browser: Here is a doc describing using the data browser.
- Note, that the description is focusing on the GUDMAP site right now, but the instructions for the Data Browser are the same for the ATLAS-D2K website.
- Policy for accessing protected human sequencing data (fastq and bam)
- Command lines and libraries
Exporting Data
Submitting Data
For members of ATLAS-D2K (specifically members of GUDMAP and RBK) to submit data, use our self-curation tools to add or edit data. Note that you must have the correct access before you are able to submit any data.
- If the type of data you need to submit is not listed below, please contact help@atlas-d2k.org.
- If you are publishing a paper using ATLAS-D2K data, it’s a good idea to contact us as well to make sure you have an appropriate Data Collection for optimal citation.
To add or edit data:
- Standard files and formats for submission
- Imaging Data (Specimen)
- Sequencing, Metabolomics, and Image Mass Cytometry Data (Study)
- Antibodies
- Cell Lines
- Data Collections (esp for publications!)
- Protocols
- Single Cell Visualization Files (draft)
- Color Palette for Image Annotation
To upload your data files in bulk:
Images and Videos
Data Publication and Citation
- How to create a collection and citation for publications
- Shortcut urls for citation and sharing - good for sharing any data record.
Access to Internal Resources
If you need access to ATLAS-D2K resources such as the ability to submit/curate data or access the Internal site, go to Accessing ATLAS-D2K Resources.