Select Dataset
Project Overview
Sample Table
Result Table
Data Table
Protein Gene Names
Upload Files
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Select data set

Demo Projects

Upload RData File

Upload Data Files (csv)

Available Dataset

Choose data file

Browse...

(Optional) Choose network file

Browse...

Use the Upload Files tab to the right to create your own data set.

Expression Data Units

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Use the boxes below to remove or add groups/samples. Use the tools at right side for advanced selection and ordering.

Select Groups

Get Samples from Comparison?

Select Samples

Genes Used for PCA Plot

All Variable

Choose Gene Number

Color By

Shape By

Size By

Select Principal Components

Plot Ellipsoid (>3 per Group)

No Yes

Show Mean Point

No Yes

Show Marginal Rugs

No Yes

Select palette

Dot Size (when size by not used):

Label Samples:

All None Subset

Label Font Size:

Select Sample Label

List of Samples to Label

Select Covariates:

Principle Component (PC) Cutoff (% explained variance)

Choose FDR Value Cutoff

Number of Columns for Plots

Plot Ellipsoid (>3 per Group)

No Yes

Dot Label

No Yes

tree cut number:

Label Font Size:

Select Plot Format

tree horizontal circular

Select Numerica Variable to Plot

Plot Height:

Plot Width:

Max # of Top Genes Per Sample:

Max # of Genes to Show

Show Table Instead of Graph?

Gene Plot Height:

Gene Plot Width:

Label Font Size:

Convert Expression Data

None log to linear

log base

small value

Label for Top Gene %

Select Principal Components

Select Number of Top Genes:

Select Gene Label

UniqueID Gene.Name

Label Font Size:

Select Principal Components

PCA Plot
Covariates
Eigenvalues
PCA Variables Plot
PCA Variables Table
PCA 3D Plot
PCA 3D Interactive
Sample-sample Distance
Dendrograms
Box Plot
CV Distribution
Help

Summary
Categorical Covariates
Numerical Covariates

After changing parameters, please click Refresh button in the Summary panel to generate new plots.

Plot Height:

After changing parameters, please click Refresh button in the Summary panel to generate new plots.

Plot Height:

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3D plot

Select Comparison Groups for Volcano Plot

1st Comparison (X-axis)

2nd Comparison (Y-aixs)

Choose Fold Change Cutoff

Choose P Value Cutoff

P value or P.adj Value?

Pval Padj

Choose TPM Cutoff

At least one group has the average TPM value >= cutoff.

Select Gene Label

Label Genes:

DEGs None Upload Geneset

# of Genes to Label

List of genes to label (UniqueID, Gene.Name or Protein.ID)

Select color scheme

Red-Green-Gray Orange-Purple-Blue

Show More Options

Yes No

Max abs(log2FC) in plot (use 0 for full range)

Max -log10(Stat Value) in plot (use 0 for full range)

Dot Size:

Label Font Size:

Legend Font Size:

Legend position

bottom right

Rasterize plot

Yes No

Make X and Y scale the same?

Yes No

Color DEGs using dot color?

Yes No

DEG Counts
Volcano Plot (Static)
Volcano Plot (Interactive)
DEGs in Two Comparisons
Data Table
Help

Click a comparison name to view volcano plot.

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Genes used for heatmap

All Subset Upload Genes Geneset

Select upload type

Gene List Annotated Gene File

Enter Gene List

Plot Random Genes or Variable Genes

Random Variable

Choose Gene Number

Select Genes from Test:

Fold Change Cutoff

P Value Cutoff

P value or P.adj Value?

Pval Padj

Choose TPM Cutoff

At least one group has the average TPM value >= cutoff.

Annotate Samples

Apply Clustering:

Apply Scaling:

Color Key:

angle of label

Column Font Size:

Row Font Size:

Set Margin Width

Set Margin Height

Color Key:

angle of label

Column Font Size:

Row Font Size:

Set Margin Width

Set Margin Height

Column Font Size:

Row Font Size:

Gene Label

Max Number of Genes to Label:

After changing parameters, please click Plot/Refresh button in the plot panel to generate heatmap.

Highlight Subset of Genes:

Yes No

Font Size:

Show More Options

Yes No

Heatmap Height:

Show row dendrogram

No Yes

Show column dendrogram

No Yes

Low

Mid

High

Distance Metric:

Linkage Algorithm:

cutree_rows:

cutree_cols:

Upload Colors for Annotations

Yes No

Row Title

Row Title Font Size:

Column Title

Column Title Font Size:

Static Heatmap Layout 1
Static Heatmap Layout 2
Interactive Heatmap
Help

Genes Used in Plot

Select Upload Genes Geneset

Enter Gene List

Select Gene Label

UniqueID Gene.Name

Gene Name (Select 1 or more)

Separate or One Plot

Separate OnePlot

Select Test

Choose Fold Change Threshold

Choose P-value Threshold

P value or P.adj Value?

Pval Padj

Choose TPM Cutoff

At least one group has the average TPM value >= cutoff.

Select Page

Plot Number per Page

Order Genes by

abs(Fold Change) P value

Select Gene Label

Select Plot Format

Box Plot Bar Plot violin line

OnePlot only supports Bar and Line plots

Show Individual Point?

YES NO

X Axis

Select and Reorder the Groups for X Axis

Convert Numeric X-axis Values to Character

Color By:

Select colour

Select palette

Axis Font Size:

Title Font Size:

Column Number

Y label

X label

X Angle

Y Axis Scale

Log Linear

Linear values are computed using the log base and samll value from the log based expression unit, e.g. log2(TPM+0.25). Please update the values below and the Y Label above as needed.

log Base

Small Value

Y Axis Range

Auto Manual

Y Min

Y Max

After changing parameters, please click Plot/Refresh button in the plot panel to generate expression plot.

Axis Font Size:

Label Font Size:

Y label

X label

X Angle

Density or histogram on Right:

densigram density histogram boxplot violin

Enter some genes in Search Expression Data tab, then come here for data table.

Browsing
Searched Expression Data
Data Table
Result Table
Rank Abundance Curve
Help

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Use subset genes or upload your own subset?

subset upload genes

Choose Fold Change Threshold

Choose P-value Threshold

P value or P.adj Value?

Pval Padj

Choose TPM Cutoff

At least one group has the average TPM value >= cutoff.

list

Select Groups (re-order under Groups and Samples tab)

Cluster Method

Soft Clustering

K-means

Cluster Number:

Font Size:

X Angle

Column Number

Data Output Format:

Wide Format Long Format

Clustering of Centroid Profiles
Data Table
Help

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