Welcome to the SWAMP-SEQ Visualization Toolkit


Differential Expression

Input results from a differential expression analysis

Interactive Tables

Review and filter differentially expressed genes

Visualizations

Plot volcano plots, heatmaps, dimensionality reduction plots and more

Downstream Analysis

Conduct downstream analysis such as enrichment analysis


The SWAMP-SEQ Visualization Toolkitis an interactive, user-friendly toolkit designed for the analysis and visualization of RNAseq data. Users can upload processed results (e.g., normalized counts, metadata, and DEG tables) or access preloaded datasets directly from HiPerGator. The platform supports a wide range of visualizations and downstream analyses, including quality control plots (PCA, MDS), heatmaps, volcano plots, differential expression summaries, and enrichment analysis. Swamp-SEQ is intended to streamline the exploration of transcriptomics results and promote reproducible, high-quality interpretation of gene expression data.

Help Center
The 'Process-Data' tab allows users to upload a normalized log-count matrix, sample metadata file, and DEG table for visualization and downstream analysis. If your analysis was performed by the UFHCC Bioinformatics team, these files will be included in your final report in the required format. If the analysis was conducted externally, please format your files according to the provided templates to ensure compatibility. Each of the remaining tabs enables interactive visualizations—such as volcano plots, heatmaps, and enrichment analysis—based on the uploaded data. You can use the sidebar filters to customize the results displayed.
For more information regarding the analysis, contact UFHCC-BCBSR@ufl.edu.



Upload Requirements and Template Format


1. Count Matrix File

• File must be in .csv or .tsv format.

• The first column should be gene identifiers labeled 'ENSEMBL'.

• Remaining columns should represent sample names in the format SampleID_Condition (e.g., KRAS01_WT, KRAS02_WT).

• Download a sample format below to ensure compatibility.

Preview: Normalized Count Matrix

2. Metadata File

• Columns must include 'Sample_Name' and 'Conditions'.

• Each row should represent a single sample and its associated experimental condition.

• Use the metadata template provided for correct formatting.

Preview: Metadata

3. DEG Table File

• You must upload a DEG table generated by either DESeq2 or limma-voom.

• Required columns for limma-voom: SYMBOL, logFC, AveExpr, t, P.value, adj.P.value, B, contrast, ensembleID.

• Required columns for DESeq2: SYMBOL, log2FoldChange, baseMean, lfcSE, stat, pvalue, padj, contrast, ensembleID.

• The column order does not matter, but names must match. One row per gene per contrast is expected.

Preview: DEG Table
Refer to the left panel to download the appropriate templates before uploading.


Volcano Plots

Use the options available on the right side corner to navigate your way on the figure.

Dimensionality Reduction

Principal Component Analysis

Multidimensional Scaling


Interactive Heatmaps


Differentially Expressed Gene Tables

View your data


Filter Options

Gene Ontology Enrichment

GO Results Table

KEGG Enrichment

KEGG Results Table


About Swamp-SEQ

Swamp-SEQ is an interactive toolkit designed by the University of Florida Health Cancer Center BCB-SR Bioinformatics group to support visualization and analysis of transcriptomics data.

It enables users to upload normalized count data, metadata, and DEG results, or access shared datasets directly from HiPerGator.

Visualizations include PCA, heatmaps, volcano plots, DEG tables, and enrichment analysis.

Developed by the UFHCC Bioinformatics and Computational Biology Shared Resource.

For support, contact UFHCC-BCBSR@ufl.edu.