CellSeekr

Discovery is CellSeekr’s exploratory mode, designed for open-ended investigation of gene expression across immune cell types using predefined analytical views — including top 50 differential gene expression, proximity mapping, UMAP visualization, and GEO exploration — with comparisons anchored to specific cell types and patient groups.

Targeted Analysis is CellSeekr’s most granular mode, designed for hypothesis-driven investigation. Unlike Discovery, it allows users to define custom immune cell signatures and query specific genes of interest, enabling precise pairwise comparisons between user-defined cell populations in the context of patient response or treatment setting.

In summary, Discovery uses predefined cell types and views to explore gene expression broadly, while Targeted Analysis gives users full control over both cell type definition and gene selection for focused, hypothesis-driven interrogation.

CellSeekr pre-defines several immune populations.

These cell types are defined according to the following signatures:

T cells: UBC+PTPRC+CD3D+NCAM1-

NK cells: UBC+PTPRC+NCAM1+CD3D-

Myeloid cells: UBC+PTPRC+CD14+

Tregs: UBC+PTPRC+CD3D+CD4+FOXP3+

M1 Macrophages: UBC+PTPRC+CD14+FCGR1A+CD80+

M2 Macrophages: UBC+PTPRC+CD14+CD163+MRC1+ 

Granulocytic MDSCs: UBC+PTPRC+CD33+HLAD-RA-FUT4+ 

Monocytic MDSCs: UBC+PTPRC+CD33+HLAD-RA-FUT4-  

CD45^– cells: UBC+PTPRC-

Immune cells: UBC+PTPRC+

Astrocytes: ATP1B2+ALDH1L1+ITGAM-PTPRC-

Neurons: RBFOX3+

All cells: UBC+

In future iterations, additional cell types will become available.

Yes. New datasets and tumor types are continuously added to CellSeekr as they become available and meet our inclusion criteria. While there is no fixed release schedule, we regularly curate and integrate high-quality public datasets to expand coverage across tumor types, experimental platforms, and cell populations.

CellSeekr is a regularly updated resource, and expanding its breadth and depth is an active priority. We encourage users to submit dataset requests or suggestions to help guide future additions.

Yes, you can request datasets to be added to CellSeekr. If you are interested in submitting a request, please submit a study request with the dataset name and the reference repository information for the desired dataset.

All plots generated within CellSeekr can be saved locally by right-clicking the image and selecting ‘Save Image As.’ The bar graphs and violin plots produced in the analysis interface at analyze.cellseekr.com can be downloaded in the same manner. Additionally, raw data underlying each plot is provided in a table format directly within the interface and can be copied for use in external visualization or statistical software such as GraphPad Prism or Microsoft Excel.

When multiple analysis requests are submitted at the same time, CellSeekr may place additional jobs in a processing queue. This ensures fair resource allocation and system stability for all users.

If your job has been queued, it will begin automatically as soon as computational resources become available. Because CellSeekr performs analyses on large-scale datasets, processing times may vary, and some requests may take several minutes to complete depending on complexity and server demand.

We appreciate your patience and are continually working to optimize performance and efficiency.

Most technical issues can be resolved by restarting the analyzer or refreshing the page. If issues persist, send us an email.

Our privacy policy can be accessed here.