CVCDAP

Toolbox Menu Onco-plot Prevalence Plot TMB Plot Mutation Signature analysis Mutual Exclusive analysis Driver Gene analysis Lollipop Plot Rainfall Plot VAF Plot TiTv Plot Onco-strip Drug-Gene Interaction Gene Cloud

Genomic Analysis Tools for Single Cohort

Gene Cloud : This tool illustrates gene mutation frequency in a cohort by a Word Cloud. Size of each gene is proportional to the number of samples harbouring somatic mutations in this gene in the given cohort.

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Select a cohort

Select a cohort for analysis (Required)

Options for plotting

minMutSamples

topN

Width

Height

Output RData file

This analysis task includes samples (sample IDs) with the required molecular and/or clinical data from the .

You can download a source file of RData format here.

The analysis parameters and result files are also available in the Analysis History for future visit.

Onco-plot : Plots a sample-level overview for top mutated genes identified in a given cohort. Each column represents a sample and each row is a gene. The top barplot shows the number of mutations for each sample, while the right barplot represents the frequency of mutations in each gene. By default, samples will be ordered by the most mutated genes.

Help

Select a cohort

Select a cohort for analysis (Required)

Options for plotting

Top

selectedGenes

Font size (Title)

Font size (Legend)

Width

Height

Output RData file

This analysis task includes samples (sample IDs) with the required molecular and/or clinical data from the .

You can download a source file of RData format here.

The analysis parameters and result files are also available in the Analysis History for future visit.

Onco-strip : This tool plots a concise sample-level mutational overview for a given set of genes.

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Select a cohort

Select a cohort for analysis (Required)

Options for plotting

topN

Genes

Font size (Title)

Font size (Legend)

Width

Height

Output RData file

This analysis task includes samples (sample IDs) with the required molecular and/or clinical data from the .

You can download a source file of RData format here.

The analysis parameters and result files are also available in the Analysis History for future visit.

TiTv Plot : This tool shows overall distribution of six types of mutational conversions including transitions (Ti) and transversions (Tv), as well as fraction of conversions in each sample.

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Select a cohort

Select a cohort for analysis (Required)

Options for plotting

Width

Height

Output RData file

This analysis task includes samples (sample IDs) with the required molecular and/or clinical data from the .

You can download a source file of RData format here.

The analysis parameters and result files are also available in the Analysis History for future visit.

VAF Plot : This tool shows variant allele frequencies (VAF) of identified somatic mutations in a boxplot, which could help estimate clonal status of given genes. In the output figure, each point represents a mutation. VAF is a measure of diploid zygosity. Without considering tumor purity and copy number alteration issues, VAF of a heterozygous loci will be near 50%, VAF of homozygous loci will be near 100%.

Help

Select a cohort

Select a cohort for analysis (Required)

Options for plotting

topN

Gene(s)

Width

Height

Output RData file

This analysis task includes samples (sample IDs) with the required molecular and/or clinical data from the .

You can download a source file of RData format here.

The analysis parameters and result files are also available in the Analysis History for future visit.

Lollipop Plot : This tool illustrates mutation frequency along protein structure by a lollipop plot, which could help identify mutation hotspots visually.

Help

Select a cohort

Select a cohort for analysis (Required)

Options for plotting

Gene

please input a gene symbol

LabelPos

Width

Height

Output RData file

This analysis task includes samples (sample IDs) with the required molecular and/or clinical data from the .

You can download a source file of RData format here.

The analysis parameters and result files are also available in the Analysis History for future visit.

Rainfall Plot : Highlights hyper-mutated genomic regions, with showing inter variant distance on a linear genomic scale, by a rainfall plot. The rainfall plot can be seen as a scatter plot showing the location of events on the x-axis versus the distance between consecutive events on the y-axis, which is mostly used for illustrating the distribution of somatic mutations along a reference genome, typically to identify events occurring at high frequency over very short distances.

Help

Select a cohort

Select a cohort for analysis (Required)

Options for plotting

Tumor Sample Barcode

Width

Height

Output RData file

This analysis task includes samples (sample IDs) with the required molecular and/or clinical data from the .

You can download a source file of RData format here.

The analysis parameters and result files are also available in the Analysis History for future visit.

Mutation Signature Analysis : This tool illustrates contribution of known mutational processes to somatic mutations identified in a cohort, which helps to understand associated mutational features and aetiology.

Help

Select a cohort

Select a cohort for analysis (Required)

Options for plotting

referenceSigs

TriCountsMethod

Width

Height

Output RData file

This analysis task includes samples (sample IDs) with the required molecular and/or clinical data from the .

You can download a source file of RData format here.

The analysis parameters and result files are also available in the Analysis History for future visit.

Drug-Gene Interaction analysis :This tool plots potential druggable mutated genes in categories, using gene druggability information from Drug-Gene Interaction database.

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Select a cohort

Select a cohort for analysis (Required)

Options for plotting

topN

Genes

Width

Height

Output RData file

This analysis task includes samples (sample IDs) with the required molecular and/or clinical data from the .

You can download a source file of RData format here.

The analysis parameters and result files are also available in the Analysis History for future visit.

Mutual Exclusive analysis: : This tool allows users to determine if query genes are mutually exclusively mutated or co-occurring by pair-wise Fisher's Exact test.

Help

Select a cohort

Select a cohort for analysis (Required)

Options for plotting

topN

Genes

Upper P-value

Lower P-value

Width

Height

Output RData file

This analysis task includes samples (sample IDs) with the required molecular and/or clinical data from the .

You can download a source file of RData format here.

The analysis parameters and result files are also available in the Analysis History for future visit.

Driver Gene analysis : This tool identifies potential driver genes in a given cohort, based on positional clustering by OncodriveCLUST and visualized by a scatter plot, in which the size of a point represents the number of clusters found in a given gene . Genes satisfying FDR thresholds are coloured in red, with others in blue.

Help

Select a cohort

Select a cohort for analysis (Required)

Options for plotting

MinMut

FDR

Width

Height

Output RData file

This analysis task includes samples (sample IDs) with the required molecular and/or clinical data from the .

You can download a source file of RData format here.

The analysis parameters and result files are also available in the Analysis History for future visit.

Prevalence Plot : This tool allows users to plot prevalence of mutations in given gene(s) for each project included in the analysis cohort.

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Select a cohort

Select a cohort for analysis (Required)

Options for plotting

Genes

Width

Height

Output RData file

This analysis task includes samples (sample IDs) with the required molecular and/or clinical data from the .

You can download a source file of RData format here.

The analysis parameters and result files are also available in the Analysis History for future visit.

TMB Plot : This tool plots and compares TMB distribution between mutant group (MT)with somatic mutations in gvien gene(s) and Wild Type (WT) group of patients.

Help

Select a cohort

Select a cohort for analysis (Required)

Options for plotting

Genes

Project

Test method

Width

Height

Output RData file

This analysis task includes samples (sample IDs) with the required molecular and/or clinical data from the .

You can download a source file of RData format here.

The analysis parameters and result files are also available in the Analysis History for future visit.