richStudio

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Welcome to richStudio

An interactive platform for functional enrichment analysis, gene set clustering, and visualization.

Run GO, KEGG, or Reactome enrichment directly, or import results from tools like clusterProfiler or DAVID. Cluster functionally related terms using multiple algorithms and explore results through interactive plots.

v0.1.6

Quick Start

Upload & Enrich

Upload DEG lists and run GO, KEGG, or Reactome enrichment.

Cluster

Import enrichment results from any tool (clusterProfiler, DAVID, etc.) or enrich here first at Step 1.

Visualize & Export

Explore interactive plots, save sessions, and export results.

Key Features

GO, KEGG, and Reactome enrichment via richR and bioAnno
Import enrichment results from any tool, or enrich here
Three clustering algorithms (Hierarchical, DAVID, richR Kappa)
Interactive bar, dot, heatmap, and network visualizations

Quick Links

About

Developed by the Hur Lab at UND School of Medicine & Health Sciences.

Team: Junguk Hur, Sarah Hong, Jane Kim, Kai Guo

Citation:
Hur J, Hong S, Kim J, Guo K. richStudio: an interactive platform for functional enrichment clustering and visualization. Manuscript in preparation.

richStudio v0.1.6 | R Shiny | GPL-3 License

File upload
Text input
Upload DEG sets

Upload files

Upload gene differential expression data from local computer

Accepted formats: .txt, .csv, .tsv

Select files

Browse...

Load demo

Loads sample DEG sets: 'deg_mouse1', 'deg_mouse2', 'deg_mouse3'

Genes can be separated by any non-alphanumeric character

Text Input

Name

Enrich

Select DEG sets to enrich

Select annotation source

Select keytype

Select ontology

Select species

DEG sets
Enrichment Results
Uploaded files

Double-click on any cell to change its value.

Preprocess data

Select DEG set

GeneID header

Filter by

Cutoff

Remove NA?

Export data

Export as

Download

Select enrichment result

Export as

Download

File upload
Text input
Load enrichment result

Upload from computer

Accepted formats: .txt, .csv, .tsv

Select files

Browse...

Load demo

Loads sample enrichment results: 'go1', 'go2', 'kegg1'

This functionality is currently not available, but will be supported in the future.

Text Input

Name

Available enrichment results

You can rename any enrichment result by double-clicking on the relevant cell.

Enrichment Result Visualization

Selection

Select enrichment result to view

Table View

No data to display

Select an enrichment result above.

Options

Select enrichment result to view

View rich score or p-value?

View Padj or Pvalue?

P-value cutoff

Number of terms to display

Bar Plot

No data to display

Select an enrichment result and configure options above.

Options

Select enrichment result to view

View Padj or Pvalue?

P-value cutoff

Number of terms to display

Dot Plot

No data to display

Select an enrichment result and configure options above.

Options

Select enrichment result to view

View Padj or Pvalue?

P-value cutoff

Number of terms to display

Network

No data to display

Select an enrichment result and configure options above.

Top terms
Custom terms

Select enrichment results

Select top terms by

P-value cutoff

Number of terms per result to display

Enrichment results in heatmap

Double click any cell to change its value.

Select enrichment result

Select top terms by

Title

Delete

Select enrichment result

Select terms to delete

Top Terms Heatmap

Custom Terms Heatmap

File upload
Text input
Upload enrichment results for clustering

Select files

Browse...

Accepted formats: .txt, .csv, .tsv

Load demo

Loads sample enrichment results: 'go1', 'go2', 'kegg1'

This functionality is currently not available, but will be supported in the future.

Text Input

Name

Double-click on any cell to change its value.

Select enrichment result

Export as

Download

Select cluster result

Export as

Download

Cluster Enrichment Results

Select enrichment results

Select enrichment results to cluster

Select one or more enrichment results to cluster together

Cluster group name

Choose a descriptive name

This name will identify the clustering result

Clustering Method

Clustering Results

Cluster Summary

Method Information

Pairwise similarity scores between terms

Detailed cluster assignments

File upload
Text input
Load cluster result

File upload for cluster results is not yet supported. Use the Clustering tab to generate results.

Select files

Browse...

This functionality is currently not available, but will be supported in the future.

Text Input

Name

Available cluster results

You can rename any cluster result by double-clicking on the relevant cell.

Cluster Result Visualization

Heatmap
Cluster info

Options

Select cluster result to view comprehensive heatmap displaying values for each cluster

Select cluster result

Select value to show

Calculate value by

Cluster Heatmap

No cluster data loaded

Select a cluster result above to view the heatmap.

Options

Select individual clusters to view heatmap of values for each term in cluster

Select individual clusters

Select value to show

Term Heatmap

No clusters selected

Select individual clusters above to view the term heatmap.

Detailed Cluster Info

View and export individual term data for cluster results

Select cluster result

Export as

Download

Manage Files

Rename or remove uploaded files and analysis results.

Rename

Rename DEG Set

Select DEG set

New name

Rename Enrichment Result

Select enrichment result

New name

Rename Cluster Result

Select cluster result

New name

Remove

Remove DEG Sets

Select DEG sets to remove

Remove Enrichment Results

Select enrichment results to remove

Remove Cluster Results

Select cluster results to remove

Save & Load Analysis Session

Save your current analysis session or load a previously saved session.

Save Session

Download your current analysis state including:

DEG sets
Enrichment results
Clustering results
Session settings

Session name

Save format:

RDS (Recommended)

JSON (Portable)

Download Session

RDS format preserves all R objects exactly. JSON format is more portable but may lose some data types.

richStudio

Welcome to richStudio

Quick Start

Key Features

Quick Links

About

Upload files

Load demo

Enrich

Preprocess data

Export data

Upload from computer

Load demo

Available enrichment results

Enrichment Result Visualization

Selection

Table View

No data to display

Options

Bar Plot

No data to display

Options

Dot Plot

No data to display

Options

Network

No data to display

Enrichment results in heatmap

Delete

Top Terms Heatmap

Custom Terms Heatmap

Load demo

Cluster Enrichment Results

Select enrichment results

Cluster group name

Clustering Method

Clustering Results

Cluster Summary

Method Information

Intermediate Results (Advanced)

Available cluster results

Cluster Result Visualization

Options

Cluster Heatmap

No cluster data loaded

Options

Term Heatmap

No clusters selected

Detailed Cluster Info

Manage Files

Rename

Rename DEG Set

Rename Enrichment Result

Rename Cluster Result

Remove

Remove DEG Sets

Remove Enrichment Results

Remove Cluster Results

Save & Load Analysis Session

Save Session

Load Session

Current Session Summary

DEG Sets

Enrichment Results

Clustering Results

Export Individual Results

Export Enrichment Result

Export Clustering Result

Export All Results