Step 1
Open the single-cell explorer
Use Single-cell in the top navigation, or the Single-cell transcriptomics card on the home page.
Tutorial
Guided use of ProMICA
Follow three visual walkthroughs: the single-cell explorer, the spatial explorer, and the LLM skill.
01
Single-cell transcriptomics
Open the explorer, colour the UMAP, plot a gene, then run contrast, correlation, or differential analysis.
02Spatial transcriptomics
Open the explorer, map cell-type annotation on a pathology section, plot a gene, then run contrast or colocalization.
03LLM-assisted exploration
Explore the atlas through an AI-assisted approach.
Walkthrough 01
Single-cell transcriptomics
Start from the home page, colour the atlas by annotation, search a gene, and continue into contrast, correlation, or differential analysis.
Step 2
Colour the UMAP by category
On the Category tab, choose an annotation level, show or hide clusters in the filter tree, and use the map tools as needed.
Step 3
Plot a gene of interest
Open the Expression tab, enter a gene symbol, then continue into expression contrast when two annotated groups are to be compared.
Step 4
Run expression contrast
Restrict the comparison if needed, define the two conditions from annotation categories, then plot the contrast.
Step 5
Open expression correlation
From the Expression tab, continue into correlation analysis to pair the plotted gene with a second gene.
Step 6
Plot pairwise expression correlation
Enter the second gene, optionally restrict the cohort, choose cell- or sample-level units, then plot the correlation.
Step 7
Open differential expression analysis
Compare two groups of cells and rank genes by differential expression, with optional pathway enrichment on the ranked list.
Step 8
Define the two groups
Optionally split cells by gene expression, restrict the cohort, assign categories to Group 1 and Group 2, then run the test.
Step 9
Run gene-set enrichment analysis
On the result page, choose a gene-set collection and run GSEA on the ranked contrast.
Step 10
Inspect selected pathways
Select one or more enriched sets and plot the running-score curves.
Walkthrough 02
Spatial transcriptomics
Map cell-type annotation or gene expression on a pathology section, then run expression contrast or spatial colocalization.
Step 1
Open the spatial explorer
Use Spatial in the top navigation, or the Spatial transcriptomics card on the home page.
Step 2
Select a pathology section
Specify the spatial transcriptomic assay, the physiological or disease state, and the pathology section, in that order.
Step 3
Colour the section by cell-type annotation
Select the annotation layer, show or hide cell types, and use the map tools as needed.
Step 4
Plot a gene of interest
Open the Expression tab, enter a gene symbol, then continue into expression contrast to compare two regions on the section.
Step 5
Run expression contrast
Draw two regions, optionally restrict each cluster to a cell type, then plot the contrast.
Step 6
Open spatial colocalization
From the Expression tab, continue into colocalization to compare the plotted gene with a second gene across sections.
Step 7
Plot colocalization
Enter the exploratory gene, restrict by disease state if needed, choose sections and colours, then plot.
Walkthrough 03
LLM-assisted exploration
Start from the home page, download the archive, and provide the complete folder to an AI assistant that can issue HTTP requests.
Step 1
Download the skill
On the home page, use Download Skill on the ProMICA Skill card to obtain the archive.
Step 2
Install in a coding assistant
Extract the archive and place the promica-skill folder in the assistant’s skills directory.
Step 3
Upload to an HTTP-capable model
Extract the archive and upload all four files to a language model that can issue HTTP requests.
