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AnnoPeak()
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Conduct Peak Annotation. |
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ConductDESeq2()
|
Conduct Differential Analysis with DESeq2. |
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ConductFE()
|
Conduct Functional Enrichment Analysis. |
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ConductGSEA()
|
Conduct Gene Set Enrichment Analysis (GSEA). |
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ContinuousColorMap()
|
Create Continuous Color Map. |
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CountQC()
|
Count QC plot. |
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DEHeatmap()
|
Heatmap for Differential Analysis Results. |
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DEbCA()
|
Integrate Differential Expression Results and Peak Annotation Results of ChIP-seq and ATAC-seq. |
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DEbDE()
|
Integrate Two Differential Expression Results. |
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DEbDEFE()
|
GO Enrichment on Two Differential Expression Integration Results. |
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DEbPeak()
|
Integrate Differential Expression Results with Peak Annotation/Differential Expression Results. |
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DEbPeakFE()
|
GO Enrichment on Integrated Results. |
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DiffPeakPie()
|
Stat Genomic Regions of Differential Peaks with Pie Plot. |
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DiscreteColorPalette()
|
Create Discrete Color Palette. |
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DownloadGEOSupp()
|
Download GEO Supplementary Files. |
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EnrichPlot()
|
Create Plot for Functional Enrichment Analysis. |
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ExportPCGenes()
|
Export selected PC genes. |
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ExtractDA()
|
Extract Differential Analysis Results. |
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ExtractGEOExp()
|
Extract Raw Count Matrix. |
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ExtractGEOExpSupp()
|
Extract Raw Count Matrix from Supplementary Files. |
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ExtractGEOInfo()
|
Extract GEO Study Information. |
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ExtractGEOMeta()
|
Extract Sample Metadata. |
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FindMotif()
|
Find Motif of Peaks from RNA-seq and Peak-related Data Integrated Results. |
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GenePlot()
|
Gene Expresion or Peak Accessibility/Binding Plot. |
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GetConsensusPeak()
|
Get Consensus Peak with MSPC. |
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GetGeneLength()
|
Get Gene Length from GTF. |
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IDConversion()
|
Gene ID Conversion. |
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InferRegulator()
|
Identify TFs from Gene Expression Reults. |
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InteDiffQuad()
|
Create Quadrant Diagram for Two Differential Analysis Integration Results. |
|
InteFE()
|
GO Enrichment on Integrated Results. |
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InteVenn()
|
Create Venn Diagram for Two Differential Analysis Integration Results. |
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LoadingGO()
|
GO enrichment on PC loading genes. |
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LoadingPlot()
|
PCA loading plot. |
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MAPlot()
|
MA-plot for Differential Analysis Results. |
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MotifCompare()
|
Map Motifs against a Motif Database. |
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MotifDiscovery()
|
de novo Motif Discovery with STREME. |
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MotifEnrich()
|
Motif Enrichment for Differentially Accessible/Binding Peaks. |
|
NetViz()
|
Visualization for Enhancer-Gene Network. |
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NormalizedCount()
|
Perform Counts Normalization. |
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OutlierDetection()
|
Detect outlier with robust PCA |
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PCA()
|
Calculate PCA. |
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PCA3D()
|
3D PCA plot. |
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PCABasic()
|
Generated PCA baisc plots, including screen plot, biplot and pairs plot. |
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ParseGEO()
|
Parse GEO Data. |
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PeakAnnoPie()
|
Create Peak Annotation Pie Plot with ggplot2. |
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PeakMatrix()
|
Prepare Count Matrix and Sample Metadata for Peak-related data. |
|
PeakProfile()
|
Create ChIP Peak Binding Profile. |
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PeakbPeak()
|
Integrate Two Peak Annotation/Differential Analysis Results. |
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PeakbPeakFE()
|
GO Enrichment on Two Peak Annotation/Differential Analysis Integration Results. |
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PlotDEbPeak()
|
Create Integrated Summary Plot. |
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ProcessEnhancer()
|
Get Near Genes of Differential Peaks. |
|
QCPCA()
|
PCA related functions used in quality control. |
|
RankPlot()
|
Rank plot for Differential Analysis Results. |
|
ReadProfile()
|
Generate Reads Profile with deepTools. |
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RunBART2()
|
Identify TFs from Gene Expression Reults with BART2. |
|
RunChEA3()
|
Identify TFs from Gene Expression Reults with ChEA3. |
|
RunTFEA()
|
Identify TFs from Gene Expression Reults with TFEA.ChIP. |
|
SampleRelation()
|
Sample to sample relationship. |
|
ScatterPlot()
|
ScatterPlot for Differential Analysis Results. |
|
VisGSEA()
|
Visualize GSEA results. |
|
VizRegulator()
|
Visualize the Identified TFs. |
|
VolcanoPlot()
|
VolcanoPlot for Differential Analysis Results. |