IDEA: Interactive Differential Expression Analyzer

Standard Comparison
Multi-factor Design
Without Replicates

Upload Data

Set Comparing Groups

Advanced

Upload Feature Length File (Optional)

Only CSV format is supported

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A feature length file can be uploaded to calculate RPKM of each feature, and should have the same number of as in count matrix.

Experimental Design

Readscount Matrix (Partly)

The first 6 rows of count matrix are shown here.

Advanced Option

Normalized Method:

Download .csv file Download Report

Calculation is in progress, please wait for a while...

Perform correlation analysis of paired samples

Spearman correlation coeffient:

DESeq Analysis Report

Calculation is in progress, please wait for a while...

Differential Expression Feature Analysis Result Table
Variance Estimation
MA Plot of Differential Expression Features

Interactive Option

FDR threshold
Normalized SizeFactors
Volcano Plot of Differential Expressed Features

Interactive Option

P.Value threshold

Fold change threshold
Heat Map of Differential Expressed Features (Partly)

Interactive Option

Numbers of features to plot:

Scale method

Cluster row/column

Show ColorKay
FDR Distribution Plot

Advanced Option

Test Method:

In DESeq2 version (1.6.2), Wald significance test is adopted by default, with likelihood ration test (LRT) as a substitute, and procedure of Benjamini and Hochberg is adopted for multiple testing.

FDR threshold

Download .csv file Download Report

EdgeR Analysis Report

Calculation is in progress, please wait for a while...

Differential Expression Feature Table
Normalized SizeFactors
Variance Estimation
MA Plot of Differential Expression Features
Volcano Plot of Differential Expressed Features

Interactive Option

P.Value threshold

Fold change threshold
Heat Map of Differential Expressed Features (Partly)

Interactive Option

Number of features to plot:

Scale method

Cluster row/column

Show ColorKay
FDR Distribution Plot

Advanced Option:

Normalized Method:

Filter your dataset by:

FDR threshold

Download .csv file Download Report

NOISeq Analysis Report

Calculation is in progress, please wait for a while...

Differential Expression Analysis Result Table
Heat Map of Differential Expressed Features (Partly)

Interactive Option

Number of features to plot:

Scale method

Cluster row/column

Show ColorKay
Probability Distribution Plot with q-value(standard comparison) or prob(without replicates)

Advanced Option

Normalized Method:

q-value

Note

In NOISeq, probability is not equivalent to pvalue, or 1-pvalue.

Download .csv file Download Report

PoissonSeq Analysis Report

test

Calculation is in progress, please wait for a while...

Differential Expression Analysis Result Table
Heat Map of Differential Expressed Features (Partly)

Interactive Option

Number of features to plot:

Scale method

Cluster row/column

Show ColorKay
Power Transformation Curve
FDR Distribution

Advanced Option

FDR threshold

Download .csv file Download Report

SAMseq Analysis Report

test

Calculation is in progress, please wait for a while...

Differential Expression Analysis Result Table
Heat Map of Differential Expressed Features (Partly)

Interactive Option

Numbers of features to plot:

Scale method

Cluster row/column

Show ColorKay
Q-Q plot
Pvalue Distribution

Advanced Option

Number of resampling procedures used to construct test statistic.

False Discovery Rate cutoff for output in significant feature table.

Pvalue threshold

Download .csv file Download Report

Intergrative Analysis

test

Calculation is in progress, please wait for a while...

Advanced Option

Rank aggregation method

Download Result(.csv format) Download Report

New analysis job

Select Experiment Type

Set Comparing Groups $(document).ready(function() {setTimeout(function() {addTooltip('tipid_5', 'Available only after DESIGN MATRIX file is properly provided ', 'right', 'hover')}, 100)});

Advanced $(document).ready(function() {setTimeout(function() {addTooltip('tipid_6', 'Click to set upload options for length file', 'right', 'hover')}, 100)});

Upload Feature Length File (Optional) $(document).ready(function() {setTimeout(function() {addTooltip('tipid_7', 'Upload feature length file in .csv format', 'right', 'hover')}, 100)});

Calculation is in progress, please wait for a while...

Samples Boxplot

Stacked Density Plot

Interactive Option

Ratio Bar Plot

Heat Map of Sample Distance

Interactive Option

Up-color

Down-color

Principal Component Analysis

Interactive Option

Correlation Analysis

Perform correlation analysis of paired samples

Interactive Option

Spearman correlation coeffient:

Feature Query - Expression Level Comparison

Interactive Option

DESeq Analysis Report

Calculation is in progress, please wait for a while...

Differential Expression Feature Analysis Result Table

Variance Estimation

MA Plot of Differential Expression Features

Interactive Option

Normalized SizeFactors

Volcano Plot of Differential Expressed Features

Interactive Option

Heat Map of Differential Expressed Features (Partly)

Interactive Option

FDR Distribution Plot

EdgeR Analysis Report

Calculation is in progress, please wait for a while...

Differential Expression Feature Table

Normalized SizeFactors

Variance Estimation

MA Plot of Differential Expression Features

Volcano Plot of Differential Expressed Features

Interactive Option

Heat Map of Differential Expressed Features (Partly)

Interactive Option

FDR Distribution Plot

NOISeq Analysis Report

Calculation is in progress, please wait for a while...

Differential Expression Analysis Result Table

Heat Map of Differential Expressed Features (Partly)

Interactive Option

Probability Distribution Plot with q-value(standard comparison) or prob(without replicates) $(document).ready(function() {setTimeout(function() {addTooltip('tipid_433', 'Please refer to NOISeq manual to understand the difference between probability and p-value.', 'left', 'hover')}, 100)});

Note

PoissonSeq Analysis Report

Calculation is in progress, please wait for a while...

Differential Expression Analysis Result Table

Heat Map of Differential Expressed Features (Partly)

Interactive Option

Power Transformation Curve

FDR Distribution

SAMseq Analysis Report

Calculation is in progress, please wait for a while...

Differential Expression Analysis Result Table

Heat Map of Differential Expressed Features (Partly)

Interactive Option

Q-Q plot

Pvalue Distribution

Intergrative Analysis

Calculation is in progress, please wait for a while...

Differentially Expressed Features Identified by Packages

Venn of DE Features Analyzed by Packages

Feature Weight Table

Set Comparing Groups

Advanced

Upload Feature Length File (Optional)

Probability Distribution Plot with q-value(standard comparison) or prob(without replicates)