Skip to content

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:

  1. 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.
  2. Select a Project — Use the Project dropdown in the sidebar to switch between saved projects. Projects with a - Not ready label are waiting for the RNA-Seq pipeline to complete. Once processing finishes, all visualization tabs become available.
  3. Explore Reports — Navigate the visualization tabs in the top navigation bar.

Report Descriptions

A table summarizing each visualization tab and its purpose:

Tab Description
PCA Sample clustering via Principal Component Analysis
Volcano Interactive volcano plot for DESeq2 differential expression results
Box Box plot of normalised count distribution per sample
Violin Violin plot of expression distribution density
Bar Filtered gene up vs down count by gene description
Heatmap by Gene Gene-level heatmap of Z-score normalised expression
Heatmap by Sample Sample-to-sample Pearson correlation heatmap
GO Gene Ontology enrichment analysis (BP, CC, MF)
KEGG KEGG pathway enrichment analysis
KEGG Pathway Map Interactive KEGG pathway network with expression overlay
PPI Protein-protein interaction network via STRING DB
Co-expression Gene correlation network from normalised counts
Venn DEG overlap across 2–3 contrasts
Enrichment Compare Cross-contrast GO/KEGG enrichment comparison heatmap
  • 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.