DEbPeak - Explore, analyze, visualize RNA-seq data and unravel the regulation of gene expression

Welcome to DEbPeak!

DEbPeak aims to explore, visualize, interpret RNA-seq data and unravel the regulation of gene expression. It contains eight functional panels:

Quality Control (QC) : QC on count matrix and samples.
Principal Component Analysis (PCA) : Visualize the PCA results, analyze the genes with large loadings of specific principal component.
Differential Expression Analysis (DEA) : Get differentially expressed genes (DEGs) and visualize the results interactively or download PDF.
Functional Enrichment Analysis (FEA) : GO enrichment analysis, KEGG enrichment analysis, Gene Set Enrichment Analysis.
Integrate with ChIP-seq (DEbChIP) : Get consensus peaks from replicates, visualize peak profile, peak annotation, integrate with RNA-seq, integration summary, GO enrichment on integrated results.
Integrate with ATAC-seq (DEbATAC) : Get consensus peaks from replicates, visualize peak profile, peak annotation, integrate with RNA-seq, integration summary, GO enrichment on integrated results, find motif on integrated results.
Integrate with ChIP-seq and ATAC-seq (DEbCA) : Integrate RNA-seq, ChIP-seq and ATAC-seq based on the peak annotation results of DEbChIP and DEbATAC, integration summary, GO enrichment on integrated results.
Utils : Useful functions when dealing with RNA-seq data, including gene name conversion (gene symbol, ENSEMBL gene ID, ENTREZ ID) and count normalization(DESeq2’s median of ratios, TMM, CPM, TPM, RPKM).

This website is free and open to all users and there is no login requirement.

Status

Last updated: 2022/12/1.

Contact

Yabing Song: songyb0519@gmail.com.

Citation

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Upload

Upload count matrix:

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Upload sample metadata:

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Column in metadata indicates condition:

Load Example Data

Download Example Data

Count Matrix

Sample Metadata

Options

Group by:

Batch by:

Options (Advanced)

Min counts:

Transform method:

Most variance genes:

Simulated number:

X axis PC:

Y axis PC:

rPCA (Outlier):

Compute PC (Outlier):

Adjust Plots

Plot Height (SampleQC):

Plot Width (SampleQC):

Plot Height (PCA):

Plot Width (PCA):

Plot Height (Outlier):

Plot Width (Outlier):

Count QC-CPM

Count QC-Saturation

Sample relationship Download PDF

Sample PCA Download PDF

Outlier detection Download PDF

Options

Group by:

Sample(s) to remove:

Options (Advanced)

Min counts:

Most variance genes:

Transform method:

Variance threshold:

X axis PC:

Y axis PC:

Top loadings:

Loading label size:

Pair PCs:

Pairs label size:

Adjust Plots

Plot Height (Biplot):

Plot Width (Biplot):

Plot Height (PairsPlot):

Plot Width (PairsPlot):

Scree Plot

Biplot Download PDF

PC pairs plot Download PDF

Options

PC (GO):

Species (GO):

Gene type:

GO type:

Options (Advanced)

PC Num:

Gene Num:

Plot column:

Gene Num (GO):

Pvalue threshold:

Padj method:

Qvalue threshold:

Plot term Num:

Term width:

Adjust Plots

Plot Height (Loading BarPlot):

Plot Width (Loading BarPlot):

Plot Height (Loading Heatmap):

Plot Width (Loading Heatmap):

Plot Height (Positive GO):

Plot Width (Positive GO):

Plot Height (Negative GO):

Plot Width (Negative GO):

Loading bar plot Download PDF

Loading heatmap Download PDF

Positive loading genes (GO table) Download table

Negative loading genes (GO table) Download table

Positive loading genes (GO plot) Download PDF

Negative loading genes (GO plot) Download PDF

Options

X axis PC:

Y axis PC:

Z axis PC:

Group by:

3D PCA

Options

Gene type:

Species:

Signif criterion:

Signif threshold:

Log2FC threshold:

All results Download table

Normalized counts Download table

Up-regulated genes Download table

Down-regulated genes Download table

Options

Visualization type:

Options (Advanced)

Point opacity:

Point size:

Fill color:

Log base:

Label key:

Scale transformation:

Visualization

Visualize

Options (Advanced)

Point opacity:

Point size:

Fill color:

Log base:

Label gene:

Top DEG Num:

Label key:

Label point size:

Label color:

Max exp:

Min exp:

Exp colormap:

Legend Position:

Legend height:

Link length:

Scale transformation:

Plot column:

Heatmap height:

Heatmap width:

Adjust Plots

Plot Height (VolcanoPlot):

Plot Width (VolcanoPlot):

Plot Height (ScatterPlot):

Plot Width (ScatterPlot):

Plot Height (MAPlot):

Plot Width (MAPlot):

Plot Height (RankPlot):

Plot Width (RankPlot):

Plot Height (GenePlot):

Plot Width (GenePlot):

Plot Height (Heatmap):

Plot Width (Heatmap):

Volcano Plot Download PDF

Scatter Plot Download PDF

MA Plot Download PDF

Rank Plot Download PDF

Gene Plot Download PDF

Heatmap Download PDF

Options

GO type:

Options (Advanced)

Pvalue threshold:

Padj method:

Qvalue threshold:

Plot term Num:

Term width:

Adjust Plots

Plot Height (Up):

Plot Width (Up):

Plot Height (Down):

Plot Width (Down):

Up-regulated genes (table) Download table

Down-regulated genes (table) Download table

Up-regulated genes (plot) Download PDF

Down-regulated genes (plot) Download PDF

Analyze

Options (Advanced)

Pvalue threshold:

Padj method:

Qvalue threshold:

Plot term Num:

Term width:

Adjust Plots

Plot Height (Up):

Plot Width (Up):

Plot Height (Down):

Plot Width (Down):

Up-regulated genes (table) Download table

Down-regulated genes (table) Download table

Up-regulated genes (plot) Download PDF

Down-regulated genes (plot) Download PDF

Upload

GMT file:

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Load Example GMT

Download Example GMT

Options (Advanced)

minGSSize:

maxGSSize:

Pvalue threshold:

Padj method:

GSEA table Download table

Options

Gene set ID:

Adjust Plots

Plot Height:

Plot Width:

GSEA Plot Download PDF

Upload

Peak file(s):

Browse...

Replicate type:

Min overlap Num:

Load Example Data

Download Example Data

Options (Advanced)

Stringency threshold:

Weak threshold:

Gamma:

Alpha:

Multiple intersections:

Consensus peaks Download table

Analyze

Options (Advanced)

Weight col:

Up dist:

Down dist:

Color:

Conf:

Up relative dist:

Down relative dist:

Bin Num:

Region type:

Gene structure:

GTF (optional):

Browse...

Adjust Plots

Heatmap Height:

Heatmap Width:

Average binding profile Height:

Average binding profile Width:

Region profile Height:

Region profile Width:

Binding heatmap Download PDF

Average binding profile Download PDF

Region profile Download PDF

Options

Up dist:

Down dist:

Seq style:

GTF (optional):

Browse...

Adjust Plots

Pie plot Height:

Pie plot Width:

Distribution plot Height:

Distribution plot Width:

Upset plot Height:

Upset plot Width:

Peak annotation results Download table

Pie plot Download PDF

Distribution plot Download PDF

Upset plot Download PDF

Options

Anno region:

Show percent:

Adjust Plots

Venn plot Height:

Venn plot Width:

Integration results Download table

Venn plot Download PDF

Options

GO type:

Options (Advanced)

Pvalue threshold:

Padj method:

Qvalue threshold:

Plot term Num:

Term width:

Adjust Plots

Plot Height (UPbChIP):

Plot Width (UPbChIP):

Plot Height (DOWNbChIP):

Plot Width (DOWNbChIP):

UPbChIP table Download table

DOWNbChIP table Download table

UPbChIP plot Download PDF

DOWNbChIP plot Download PDF

Upload

Peak file(s):

Browse...

Replicate type:

Min overlap Num:

Load Example Data

Download Example Data

Options (Advanced)

Stringency threshold:

Weak threshold:

Gamma:

Alpha:

Multiple intersections:

Consensus peaks Download table

Analyze

Options (Advanced)

Weight col:

Up dist:

Down dist:

Color:

Conf:

Up relative dist:

Down relative dist:

Bin Num:

Region type:

Gene structure:

GTF (optional):

Browse...

Adjust Plots

Heatmap Height:

Heatmap Width:

Average binding profile Height:

Average binding profile Width:

Region profile Height:

Region profile Width:

Binding heatmap Download PDF

Average binding profile Download PDF

Region profile Download PDF

Options

Up dist:

Down dist:

Seq style:

GTF (optional):

Browse...

Adjust Plots

Pie plot Height:

Pie plot Width:

Distribution plot Height:

Distribution plot Width:

Upset plot Height:

Upset plot Width:

Peak annotation results Download table

Pie plot Download PDF

Distribution plot Download PDF

Upset plot Download PDF

Options

Anno region:

Show percent:

Adjust Plots

Venn plot Height:

Venn plot Width:

Integration results Download table

Venn plot Download PDF

Options

GO type:

Options (Advanced)

Pvalue threshold:

Padj method:

Qvalue threshold:

Plot term Num:

Term width:

Adjust Plots

Plot Height (UPbATAC):

Plot Width (UPbATAC):

Plot Height (DOWNbATAC):

Plot Width (DOWNbATAC):

UPbATAC table Download table

DOWNbATAC table Download table

UPbATAC plot Download PDF

DOWNbATAC plot Download PDF

Options

Anno region:

Show percent:

Adjust Plots

Venn plot Height:

Venn plot Width:

Integration results Download table

Venn plot Download PDF

Options

GO type:

Options (Advanced)

Pvalue threshold:

Padj method:

Qvalue threshold:

Plot term Num:

Term width:

Adjust Plots

Plot Height (UPbChIP):

Plot Width (UPbChIP):

Plot Height (DOWNbChIP):

Plot Width (DOWNbChIP):

UPbCA table Download table

DOWNbCA table Download table

UPbCA plot Download PDF

DOWNbCA plot Download PDF

Upload

File:

Browse...

Load Example Data

Download Example Data

Options

Gene type:

Species:

Conversion results Download table

Upload

Upload count matrix:

Browse...

Upload sample metadata:

Browse...

Gene length file (optional):

Browse...

Load Example Data

Download Example Data

Options

Column in metadata indicates condition:

Normalization method:

Normalized counts Download table

FAQ

1. How to deal with edgeR results?

DEbPeak is compatible with DESeq2 and edgeR . In this interactive interface, it uses DESeq2 internally, for user with edgeR results, the R package is an ideal choice.

2. How to obtain the R package?

DEbPeak is now available on Github , and is going to Bioconductor .

Welcome to DEbPeak!

Status

Contact

Citation

Upload

Upload count matrix: Browse...

Upload count matrix:

Upload sample metadata: Browse...

Upload sample metadata:

Column in metadata indicates condition: {"plugins":["selectize-plugin-a11y"]}

Column in metadata indicates condition:

Load Example Data

Download Example Data

Upload

Count Matrix

Sample Metadata

Options

Group by: {"plugins":["selectize-plugin-a11y"]}

Group by:

Batch by: {"plugins":["selectize-plugin-a11y"]}

Batch by:

Options (Advanced)

Min counts:

Min counts:

Transform method: rlog vst ntd {"plugins":["selectize-plugin-a11y"]}

Transform method:

Most variance genes:

Most variance genes:

Simulated number:

Simulated number:

X axis PC:

X axis PC:

Y axis PC:

Y axis PC:

rPCA (Outlier): PcaGrid PcaHubert {"plugins":["selectize-plugin-a11y"]}

rPCA (Outlier):

Compute PC (Outlier):

Compute PC (Outlier):

Adjust Plots

Plot Height (SampleQC):

Plot Width (SampleQC):

Plot Height (PCA):

Plot Width (PCA):

Plot Height (Outlier):

Plot Width (Outlier):

Count QC-CPM

Count QC-Saturation

Sample relationship Download PDF

Sample PCA Download PDF

Outlier detection Download PDF

Options

Group by: {"plugins":["selectize-plugin-a11y"]}

Group by:

Sample(s) to remove: {"plugins":["selectize-plugin-a11y"]}

Sample(s) to remove:

Run

Options (Advanced)

Min counts:

Min counts:

Most variance genes:

Most variance genes:

Transform method: rlog vst ntd {"plugins":["selectize-plugin-a11y"]}

Transform method:

Variance threshold:

Variance threshold:

X axis PC:

X axis PC:

Y axis PC:

Y axis PC:

Top loadings:

Top loadings:

Loading label size:

Loading label size:

Pair PCs:

Pair PCs:

Pairs label size:

Pairs label size:

Adjust Plots

Plot Height (Biplot):

Plot Width (Biplot):

Upload count matrix:

Browse...

Upload sample metadata:

Browse...

Column in metadata indicates condition:

Group by:

Batch by:

Transform method:

rPCA (Outlier):

Group by:

Sample(s) to remove:

Transform method:

Species (GO):

Gene type:

GO type:

Padj method:

Group by:

Gene type:

Species:

Signif criterion: