quick help guide
What can CellSeekr do?
CellSeekr is a powerful platform for highly granular discovery of gene identities in cancer. Previously, investigations of this kind were either not available or required extensive computational expertise. Use this guide to explore some key capabilities.
TARGETED ANALYSIS
Measure and compare gene expression
How do I measure and compare the expression of custom genes or gene signatures in immune cells across specific patient groups?
Use Targeted Analysis: Standard
More details
1. Navigate
2. Select
Study, cell type and gene(s). See instructions here.
3. Plot
CellSeekr generates a bar graph based on the selected parameters, quantifying gene expression within chosen immune cell types across patient groups.
4. Export
Click “Export HD figure” for high-resolution image
TARGETED ANALYSIS
Correlate cell to gene in tumor
How do I correlate the expression of a gene to an immune cell, or to another gene, in a patient group?
Use Targeted Analysis: Correlation
More details
1. Navigate
2. Select
Study, cells and/or genes to correlate. See instructions here.
3. Plot
CellSeekr generates a Pearson correlation graph displaying the correlation between selected cells and/or genes
4. Export
Click “Export HD figure” for high-resolution image
DISCOVERY ANALYSIS
Discover which cells express a gene
How do I find out which cells express a custom gene in a specific patient population?
Use Discovery Analysis: Signature to Cell Tethering
More details
1. Navigate
2. Select
Study, cell type and gene(s). See instructions here.
3. Plot
CellSeekr generates a Proportional Expression per Cell Type and Ranking leaderboard, a Top Phenotypes graph as well as Significance leaderboard and a Gene expression per group graph.
4. Export
Click “Export HD figure” for high-resolution image(s).
DISCOVERY ANALYSIS
Compare cell states in a tumor
How do I compare immune cell states in a tumor and in patient groups?
Use Discovery Analysis: Geo Cluster Explorer
More details
1. Navigate
2. Select
Study and cell type. See instructions here.
3. Plot
CellSeekr generates a Geometric Cluster Map and Patient-level GEO cluster composition graphs, which can be further customized to display specific immune cell subtypes directly from the page.
4. Export
Click “Export HD figure” for high-resolution image(s).
DISCOVERY ANALYSIS
Spatially correlate genes
How do I determine whether a custom gene+immune cell is closer to one immune+gene neighbor versus another?
Use Discovery Analysis: Proximity Mapper
More details
1. Navigate
2. Select
Study, query and two reference genes and cells. See instructions here.
3. Plot
CellSeekr will generate a Proximity Spectrum per group, and two UMAPs, one for each comparison group selected.
4. Export
Click “Export HD figure” for high-resolution image(s).
Still confused?
If you still have questions about how to use CellSeekr or its capabilities, check out the Documentation, How to Guides, or the Frequently Asked Questions. If you are still stuck, try it out and play around with it – CellSeekr is designed to be user friendly. Finally, if you still have questions – get in touch.