PanKbase is a comprehensive, centralized resource for the study of the human pancreas and diabetes. The PanKbase collective aims to integrate diverse type 1 diabetes (T1D) datasets with expert-curated knowledge in a centralized, open-source data hub. Since users will ultimately be able to contribute their own data, this will be a repository for reproducible, collaborative research within the pancreas and T1D realms.
PanKbase plans to offer integrated and computation-ready genomic, epigenomic, transcriptomic, imaging, and physiological data. Datasets are currently sourced from key external programs, from which human donor-derived pancreatic data and metadata are aggregated, harmonized, and disseminated.
Read more at https://www.pankbase.org/projects.html.
We have a discussion forum set up at https://github.com/PanKbase/external-feedback/discussions.
- View our Platform repositories
- View our Pipeline repositories
- View our PankGraph repositories
| Repository | Description |
|---|---|
| PanKbase UI | Vue‑based portal powering the main PanKbase website (pankbase.org), forked from Broad Institute’s dig‑dug‑portal. |
| PanKbase donor summary | R Shiny app summarizing donor metadata and clinical info. |
| PanKbase PCA Explorer | This is the Shiny application that runs the PCA Explorer Tool for PanKbase. |
| Data Library UI | Next.js‑based Data Library UI used by PanKbase, forked from IGVF‑DACC’s interface. |
| Data Library Metadata Database | Metadata database for the PanKbase project, forked from IGVF‑DACC/igvfd. |
| pankbase client openapi spec | OpenAPI specification defining the REST API for the PanKbase data Library. |
| pankbase python client | Auto‑generated Python client library for the PanKbase Data Library API. |
| cdk prod | CDK infrastructure repo for deploying PanKbase Data Library services in the prod AWS account. |
| PanKbase Data Library Scripts | Jupyter notebooks and scripts for analyzing datasets within PanKbase Data Library via. API interactions. |
| Repository | Description |
|---|---|
| PanKbase scRNA seq | Code and docs for replicating PanKbase’s islet single-cell RNA‑seq map. |
| PanKbase DEG analysis | Jupyter notebooks & code to replicate differential expression (DEG) analysis on PanKbase. |
| snRNAseq NextFlow | A Nextflow pipeline for processing 10X single-nucleus RNA‑seq data. |
| PanKbase RNA-seq | Bulk RNA‑seq pipeline to process PanKbase data forked from GTEx Consortium: alignment, quantification, QC in Docker/WDL. |
| PanKbase snATAC-seq pipeline | Pipeline for single‑cell ATAC‑seq data. |
| Repository | Description |
|---|---|
| PanKgraph finemap coloc | Jupyter notebooks & code for fine-mapping and colocalization analyses in PanKbase & PanKgraph. |
(Last edited on June 18, 2025)
