Files in steverozen/mSigAct.server
Shiny Server for Analyzing Mutational Signature Activities
.Rbuildignore
.gitattributes
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/ShowSpectraUI.R
R/SignatureAttributionUI.R
R/UploadSpectraUI.R
R/app_config.R
R/app_server.R
R/app_ui.R
R/golem_utils_ui.R
R/run_app.R
R/server_related_functions.R
R/signature_subsets.R
R/sysdata.rda
R/ui_related_functions.R
README.Rmd
README.md
app.R
appveyor.yml
data-raw/.travis.yml
data-raw/ICAMS.shiny-testdata/MutectVCF-GRCh37/Mutect.GRCh37.s1.vcf
data-raw/ICAMS.shiny-testdata/MutectVCF-GRCh37/Mutect.GRCh37.s2.vcf
data-raw/ICAMS.shiny-testdata/MutectVCF-GRCh38/Mutect.GRCh38.s1.vcf
data-raw/ICAMS.shiny-testdata/MutectVCF-GRCm38/Mutect.GRCm38.s1.vcf
data-raw/ICAMS.shiny-testdata/StrelkaIDVCF-GRCh37/Strelka.ID.GRCh37.s1.vcf
data-raw/ICAMS.shiny-testdata/StrelkaIDVCF-GRCh37/Strelka.ID.GRCh37.s2.vcf
data-raw/ICAMS.shiny-testdata/StrelkaIDVCF-GRCh38/Strelka.ID.GRCh38.s1.vcf
data-raw/ICAMS.shiny-testdata/StrelkaIDVCF-GRCm38/Strelka.ID.GRCm38.s1.vcf
data-raw/ICAMS.shiny-testdata/StrelkaSBSVCF-GRCh37/Strelka.SBS.GRCh37.s1.vcf
data-raw/ICAMS.shiny-testdata/StrelkaSBSVCF-GRCh37/Strelka.SBS.GRCh37.s2.vcf
data-raw/ICAMS.shiny-testdata/StrelkaSBSVCF-GRCh38/Strelka.SBS.GRCh38.s1.vcf
data-raw/ICAMS.shiny-testdata/StrelkaSBSVCF-GRCm38/Strelka.SBS.GRCm38.s1.vcf
data-raw/ICAMS.shiny_0.0.2.pdf
data-raw/PCAWG7-ColoRect-AdenoCA-ten-samples.csv
data-raw/PCAWG7-Liver-HCC-ten-samples.csv
data-raw/PCAWG7-Lung-AdenoCA-ten-samples.csv
data-raw/UI-code/checkBoxGroupInput.R
data-raw/UI-code/list-of-tabpanels.R
data-raw/mSigActWebServer.pdf
data-raw/package-data-related/code/create-COSMICv3-signatures.R
data-raw/package-data-related/code/create-COSMICv3-sigs-URL.R
data-raw/package-data-related/code/create-COSMICv3-sigs-aetiology-info.R
data-raw/package-data-related/code/create-example-spectra.R
data-raw/package-data-related/code/create-package-data.R
data-raw/package-data-related/code/create-sigs-etiology-data.R
data-raw/package-data-related/code/create-thumbnail-pictures.R
data-raw/package-data-related/data/COSMIC-v3-DBS-proposed-aetiology-short-form.csv
data-raw/package-data-related/data/COSMIC-v3-DBS-proposed-aetiology.csv
data-raw/package-data-related/data/COSMIC-v3-ID-proposed-aetiology-short-form.csv
data-raw/package-data-related/data/COSMIC-v3-ID-proposed-aetiology.csv
data-raw/package-data-related/data/COSMIC-v3-SBS-proposed-aetiology-short-form.csv
data-raw/package-data-related/data/COSMIC-v3-SBS-proposed-aetiology.csv
data-raw/package-data-related/data/COSMICv3_genome_SBS96.csv
data-raw/package-data-related/data/sigProfiler_ID_signatures_ID18.csv
data-raw/set-up.R
data-raw/test-code/test-MAP-all-tested.R
data-raw/test-code/test-compare-reconstructed.sigs.R
data-raw/test-code/test-sigminer.R
data-raw/test-code/test-signature-attribution-2.R
data-raw/test-code/test-signature-attribution-DBS78.R
data-raw/test-code/test-signature-attribution-ID.R
data-raw/test-code/test-signature-attribution-SBS96.R
data-raw/test-run-app.R
data-raw/test-run-app2.R
data-raw/website.txt
dev/01_start.R
dev/02_dev.R
dev/03_deploy.R
dev/run_dev.R
inst/WORDLIST
inst/app/COSMIC/hg19/exome/DBS78/DBS1.png
inst/app/COSMIC/hg19/exome/DBS78/DBS10.png
inst/app/COSMIC/hg19/exome/DBS78/DBS11.png
inst/app/COSMIC/hg19/exome/DBS78/DBS2.png
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inst/app/COSMIC/hg19/exome/SBS192/SBS1.png
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inst/app/COSMIC/hg19/exome/SBS192/SBS29-E.png
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inst/app/COSMIC/hg19/exome/SBS192/SBS44.png
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inst/app/www/favicon.ico
inst/app/www/msigact-overview.PNG
inst/app/www/rozen-mut-sig-collage.png
inst/app/www/test.html
inst/app/www/test.js
inst/extdata/DBS78-mSigAct-example-spectra.csv
inst/extdata/ID-mSigAct-example-spectra.csv
inst/extdata/SBS192-mSigAct-example-spectra.csv
inst/extdata/SBS96-mSigAct-example-spectra.csv
inst/extdata/mSigAct-example-VCFs.zip
inst/extdata/mSigAct-example-spectra.zip
inst/extdata/mouse-aflatoxin-VCFs/QSS20-var10-filter_AH12_FINAL-nf-anno.vcf
inst/extdata/mouse-aflatoxin-VCFs/QSS20-var10-filter_AH7_FINAL-nf-anno.vcf
inst/golem-config.yml
inst/guides/Guide.to.generating.catalogs.Rmd
inst/guides/Guide.to.generating.catalogs.md
inst/guides/Guide.to.signature.attribution.Rmd
inst/guides/Guide.to.signature.attribution.md
inst/guides/VCF-to-spectra.guide-images.pptx
inst/guides/VCF-to-spectra.guide-images/Slide1.PNG
inst/guides/VCF-to-spectra.guide-images/Slide10.PNG
inst/guides/VCF-to-spectra.guide-images/Slide11.PNG
inst/guides/VCF-to-spectra.guide-images/Slide12.PNG
inst/guides/VCF-to-spectra.guide-images/Slide13.PNG
inst/guides/VCF-to-spectra.guide-images/Slide14.PNG
inst/guides/VCF-to-spectra.guide-images/Slide2.PNG
inst/guides/VCF-to-spectra.guide-images/Slide3.PNG
inst/guides/VCF-to-spectra.guide-images/Slide4.PNG
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inst/guides/VCF-to-spectra.guide-images/Slide8.PNG
inst/guides/VCF-to-spectra.guide-images/Slide9.PNG
inst/guides/attribution-guide.pptx
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inst/guides/attribution.guide/Slide10.PNG
inst/guides/attribution.guide/Slide11.PNG
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inst/guides/attribution.guide/Slide8.PNG
inst/guides/attribution.guide/Slide9.PNG
inst/guides/general.guide.Rmd
inst/guides/general.guide.md
inst/guides/general.guide_files/figure-markdown_strict/DBS1-1.png
inst/guides/general.guide_files/figure-markdown_strict/ID6-1.png
inst/guides/general.guide_files/figure-markdown_strict/SBS1-1.png
inst/guides/mSigActWebServer.png
inst/guides/mSigActWebServer.pptx
inst/guides/mutograph.png
mSigAct.server.Rproj
man/AddNotifications.Rd
man/AddRunInformation.Rd
man/CancerTypeToSigSubset.Rd
man/CatchToList.Rd
man/GenerateZipFileFromVCFs.Rd
man/GetNamesOfVCFs.Rd
man/GetTumorColNames.Rd
man/PlotListOfCatalogsToPdf.Rd
man/PrepareExampleSpectra.Rd
man/PrepareExampleVCFs.Rd
man/ProcessVCFs.Rd
man/RemoveAllNotifications.Rd
man/TransCountsCatalogToDensity.Rd
man/UpdateNotificationIDs.Rd
man/run_app.Rd
tests/testthat.R
tests/testthat/apps/app.R
tests/testthat/apps/tests/mutect.test.R
tests/testthat/apps/tests/strelka.id.test.R
tests/testthat/apps/tests/strelka.sbs.test.R
tests/testthat/test-golem-recommended.R
