DEbPeak aims to explore, visualize, interpret RNA-seq data and decipher gene regulation network. It contains eight functional panels:

  • Quality Control (QC) : QC on count matrix and samples.

  • Principal Component Analysis (PCA) : visualize and interpret PCA results.

  • Differential Expression Analysis (DEA) : get differentially expressed genes (DEGs) and visualize the results.

  • Functional Enrichment Analysis (FEA) : GO enrichment analysis, KEGG enrichment analysis, Gene Set Enrichment Analysis.

  • Integrate with ChIP-seq (DEbChIP) : get consensus peaks, peak profile plots, peak annotaion, integrate with RNA-seq, integrate summary, GO enrichment on integrated results.

  • Integrate with ATAC-seq (DEbATAC) : get consensus peaks, peak profile plots, peak annotaion, integrate with RNA-seq, integrate summary, GO enrichment on integrated results, find motif on integrated results.

  • Integrate with ChIP-seq and ATAC-seq (DEbCA) : get consensus peaks, peak profile plots, peak annotaion, integrate RNA-seq, ChIP-seq and ATAC-seq, integrate summary, GO enrichment on integrated results.

  • Utils : useful functions when dealing with RNA-seq data, including gene name conversion and count normalization(DESeq2’s median of ratios, TMM, CPM, TPM, RPKM).

Last updated: 2022/11/13.

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Count Matrix

Sample Metadata

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Count QC-CPM

Count QC-Saturation

Sample relationship     Download PDF

Sample PCA     Download PDF

Outlier detection     Download PDF

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Scree Plot

Biplot     Download PDF

PC pairs plot     Download PDF

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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

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3D PCA

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All results     Download table

Normalized counts     Download table

Up-regulated genes     Download table

Down-regulated genes     Download table

Visualize

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Volcano Plot

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MA Plot

Rank Plot

Visualize

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Volcano Plot     Download PDF

Scatter Plot     Download PDF

MA Plot     Download PDF

Rank Plot     Download PDF

Gene Plot     Download PDF

Heatmap     Download PDF

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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

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Up-regulated genes (table)     Download table

Down-regulated genes (table)     Download table

Up-regulated genes (plot)     Download PDF

Down-regulated genes (plot)     Download PDF

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GSEA table     Download table

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GSEA Plot     Download PDF

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Consensus peaks     Download table

Analyze

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Binding heatmap     Download PDF

Average binding profile     Download PDF

Region profile     Download PDF

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Peak annotation results     Download table

Pie plot     Download PDF

Distribution plot     Download PDF

Upset plot     Download PDF

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Integration results     Download table

Venn plot     Download PDF

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UPbChIP table     Download table

DOWNbChIP table     Download table

UPbChIP plot     Download PDF

DOWNbChIP plot     Download PDF

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Consensus peaks     Download table

Analyze

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Binding heatmap     Download PDF

Average binding profile     Download PDF

Region profile     Download PDF

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Peak annotation results     Download table

Pie plot     Download PDF

Distribution plot     Download PDF

Upset plot     Download PDF

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Integration results     Download table

Venn plot     Download PDF

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UPbATAC table     Download table

DOWNbATAC table     Download table

UPbATAC plot     Download PDF

DOWNbATAC plot     Download PDF

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UPbATAC motifs     Download TAR

DOWNbATAC motifs     Download TAR

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Integration results     Download table

Venn plot     Download PDF

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UPbCA table     Download table

DOWNbCA table     Download table

UPbCA plot     Download PDF

DOWNbCA plot     Download PDF

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Conversion results     Download table

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Normalized counts     Download table

FAQ

1. How to deal with edgeR results?

DEbPeak is designed to assist in differential expression analysis, it 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 .

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