In steverozen/mSigAct.server: Shiny Server for Analyzing Mutational Signature Activities

knitr::opts_chunk$set(echo = TRUE)

Table of contents

• Introduction
• Input
• Test and example data
• Select the reference genome
• Select the genomic region
• Select the variant caller
• Optionally rename the samples
• Select and upload one or more VCFs
• Create the spectra catalogs
• Examine the spectra
• Signature attribution

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Guide to generating spectrum catalogs and plots from VCFs in the mSigAct web server{target="_blank"}

Introduction

The function of the tab "Generate spectrum catalogs from VCFs" is, to generate spectrum catalogs from VCFs and also to plot the spectra.

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The input area for uploading VCFs

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Test and example data

These buttons provide some pre-loaded example data and several test VCFs that you can download and then re-upload.

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Select the reference genome

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Select the genomic region

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Select the variant caller

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Optionally rename the samples

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Select and upload one or more VCFs

VCF formats are only partly standardized; please contact us if mSigAct has difficulty analyzing your VCF.

knitr::include_graphics("VCF-to-spectra.guide-images/Slide6.PNG")

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After the upload is complete, create the spectra catalogs

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Once the catalogs are created, optionally examine the spectra

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SBS96 and SBS192 spectra

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SBS1536 and DBS79 spectra

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DBS136 spectrum

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Simplified DBS144 spectrum and indel spectrum

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You can go to signature attribution any time after the catalogs are created

knitr::include_graphics("VCF-to-spectra.guide-images/Slide14.PNG")

steverozen/mSigAct.server documentation built on July 9, 2023, 4:52 a.m.