5-base DNA Methylation

Methylation CpGs Count Matrix

Examples of methylation CpGs count matrix are 5-base Methylation, Filtered counts. Analysis tasks that can be invoked from the methylation count matrix are listed below.

Task Menu Section	Analysis Task Name
Annotation/Metadata	Publish attributes to study
QA/QC	5-base methylation QC
Pre-analysis tools	Annotate features Generate methylation ratio
Filtering	Filter features Filter samples Split by attribute
Statistics	Differential methylation Detect differential methylation
Exploratory analysis	Graph-based clustering K-means clustering Compare clusters PCA t-SNE UMAP Hierarchical clustering / heatmap SVD
Region analysis	Get Regional Methylation
Conversion	Export matrix

Methylation Regions Count Matrix

For regional methylation data, such as those generated from the Get Regional Methylation task, the following tasks can be initiated from the regions count matrix.

Task Menu Section	Analysis Task Name
Annotation/Metadata	Publish attributes to study
QA/QC	Feature distribution
Pre-analysis tools	Generate methylation mvalues
Statistics	Correlation Detect differential methylation Descriptive statistics
Exploratory analysis	K-means clustering Compare clusters PCA t-SNE UMAP
Region analysis	Annotate regions
Motif detection	Detect de novo motifs Search for known motifs
Biological interpretation	GSEA Gene set ANOVA
Conversion	Export matrix

PCA

Analysis tasks that can be invoked from PCA data node are listed below.

Task Menu Section	Analysis Task Name
Annotation/Metadata	Publish attributes to study
Batch removal	General linear model Harmony
Statistics	Differential analysis Correlation Descriptive statistics Compute biomarkers Cox Regression Kaplan-Meier
Exploratory analysis	Graph-based clustering K-means clustering Compare clusters t-SNE UMAP Find multimodal neighbors SVD
Conversion	Export matrix

Differential Methylation Analysis Result

Analysis tasks that can be invoked from differential methylated regions analysis (e.g., DSS, Detect differential methylation) are listed below.

Task Menu Section	Analysis Task Name
QA/QC	Feature distribution
Filtering	Differential analysis filter
Statistics	Descriptive statistics
Exploratory analysis	Hierarchical clustering / heatmap Merge differential expression results
Region analysis	Annotate regions
Motif detection	Detect de novo motifs Search for known motifs
Biological interpretation	Gene set enrichment Correlation Engine atlases Correlation Engine pathways

DNA Variants

Task Menu Section	Analysis Task Name
Exploratory analysis	Chromosome view
Variant analysis	View variants Annotate variants Annotate variants (SnpEff) Annotate variants (VEP) Filter variants Summarize cohort mutations Create genotype matrix Filter variants with databases Split variants

Annotated Features

Examples of annotated features are annotated methylation regions, and annotated variants. Depends on the feature type, different analysis tasks can be invoked from the annoated features data. For example, for annotated methylation regions generated from Get Regional Methylation task, analysis that can be invoked from this annotated features data are similar to the Methylation Regions Count Matrix. For annotated variants, analysis that can be invoked from this data are similar to the DNA variants.

Analysis task that is common across the feature types is listed below.

Task Menu Section	Analysis Task Name
Combine multiomics data	Combine 5-base methylation and variant data