Instruction — Getting Started Guide¶
Header: Instruction
The Instruction tab is the default landing page after login. It provides a built-in quick-start reference with three sections:
Getting Started¶
A numbered guide walking you through the core workflow:
- Create a Project — Click New Project in the sidebar, enter NCBI accession IDs (e.g.,
PRJNA288044) and a project name, click Fetch to retrieve SRA run metadata, annotate runs with Sample Name, Group Name, and Treat/Control labels, define contrasts (Reference vs Target), and click Done to save and submit the project for RNA-Seq analysis. - Select a Project — Use the Project dropdown in the sidebar to switch between saved projects. Projects with a
- Not readylabel are waiting for the RNA-Seq pipeline to complete. Once processing finishes, all visualization tabs become available. - Explore Reports — Navigate the visualization tabs in the top navigation bar.
Report Descriptions¶
A table summarizing every report and its purpose. Click a report name for full details.
| Report | Purpose — when to use it |
|---|---|
| Project Summary | Project metadata, contrasts, samples, and downloadable data files |
| Analysis Overview (Summary) | One-glance DEG counts and distributions across all contrasts |
| PCA | QC: check replicate clustering, group separation, and outliers |
| Box & Violin | QC: verify comparable expression distributions per group |
| Heatmap by Sample | QC: sample-to-sample correlation; spot outliers/batch effects |
| Volcano | Headline DE view: which genes changed, how much, how significantly |
| MA | Fold change vs mean expression; check abundance-dependent bias |
| Bar | Up vs down gene counts by functional description |
| Gene Card | Deep-dive one gene across all contrasts and samples |
| Gene Trend | Line plots of gene expression across time-series/dose-response |
| Contrast Scatter | Compare log2FC between two contrasts (concordance/discordance) |
| Heatmap by Gene | Z-score expression patterns; clusters of co-expressed genes |
| Clustering | K-means gene clusters by response profile (time/dose series) |
| Circos | Circular summary of fold change, significance, and enrichment |
| GO | Gene Ontology enrichment (BP, CC, MF) among DEGs |
| KEGG | KEGG pathway enrichment among DEGs |
| KEGG Pathway Map | Interactive pathway diagram with expression overlaid |
| Enrichment Compare | Cross-contrast GO/KEGG enrichment comparison heatmap |
| PPI | Protein-protein interaction network via STRING DB |
| Co-expression | Correlation network from counts (API-free PPI alternative) |
| Hub Network | Rank hub genes and inspect their ego-networks |
| Venn | DEG overlap across 2–4 contrasts |
| Upset | DEG intersections across many (5+) contrasts |
| Feedback | Send bug reports, feature requests, or questions |
Sidebar Controls Summary¶
- Project — Switch between saved analysis projects
- Contrast — Select which DESeq2 contrast to display (appears when multiple contrasts exist)
- Filters — Adjust p-value and log2 fold change thresholds, Top N, filter or highlight genes by ID or description
- PCA Axes — Select principal components for X and Y axes
- Appearance — Customize dot size, plot dimensions, colors (Up, Down, Select, Others, Title, BG, Axis), font size/color, and threshold line style/color
- Presets — One-click styles: Publication, Presentation, Screen, or Reset to defaults
- New Project — Create a new analysis project from NCBI accession data
Need Help?¶
Contact information for Liragen support.