Files in acc-bioinfo/TMBleR
Tumor Mutational Burden Quantification From Gene Panels And WES

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DESCRIPTION

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NAMESPACE

NEWS.md R/annotateTMB.R R/applyFilters.R R/applySimulatePanel.R R/applyTMB.R R/callFilters.R R/callTMB.R R/compareROC.R R/compareTMBdistributions.R R/correlateTMBvalues.R R/data.R R/fetch_filtered_SNV.R R/filterByVAF.R R/filterCOSMIC.R R/filterTruncatingTumorSuppr.R R/filterVariantType.R R/generateBoxplot.R R/generateROC.R R/globalVariables.R R/inputToTMB.R R/plotTMB.R R/readCOSMIC.R R/readDesign.R R/readVcfFiles.R R/removeCancerVariants.R R/remove_non_coding_SNV.R R/simulatePanel.R R/vcf_validator.R README.md

TMBleR.Rproj

_pkgDown.yml

data-raw/.gitattributes

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data-raw/ExamplePaneldesign.bed

data-raw/ExampleVcfDatasets.R

data-raw/ExampleWESdesign.bed

data-raw/ExampleWESdesign_OnlyChr7ForTest.bed

data-raw/Example_designs.R

data-raw/Hellman_CancerCell_2018__Mutations.txt

data-raw/HumanTS.R

data-raw/HumanTumorSuppressors_from_TSGene2

data-raw/ObjectsForTests.R

data-raw/Sample1_ExampleWES_chr7.vcf

data-raw/Sample2_ExampleWES_chr7.vcf

data-raw/Sample3_ExampleWES_chr7.vcf

data-raw/Sample4_ExampleWES_chr7.vcf

data-raw/test_paneldesign.bed

data-raw/testset_1.vcf

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data/COSMIC_hg19_demo.rda

data/COSMIC_hg38_demo.rda

data/ExamplePaneldesign.rda

data/ExampleWESdesign.rda

data/ExampleWESvcfs.rda

data/Hellman_SimulatedFM1Panel_WES.rda

data/HumanTumorSuppressors.rda

data/TMB_Horizon.rda

data/TMB_VanAllen.rda

data/TMBs_SimulatedPanel.rda

data/TMBs_WES.rda

data/VanAllen_Clinical.rda

data/vcfs_NoCancer_ForPanel.rda

data/vcfs_all.rda

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inst/extdata/HorizonFFPEmild_ExamplePanel_OnlyChr5and7ForTest.vcf

inst/extdata/MskImpactPanel_468GenesMutsAndCNA.txt

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inst/extdata/Sample1_ExampleWES_chr7.vcf

inst/extdata/Sample2_ExampleWES_chr7.vcf

inst/extdata/Sample3_ExampleWES_chr7.vcf

inst/extdata/Sample4_ExampleWES_chr7.vcf

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inst/extdata/TestBED_WrongChr.bed

inst/extdata/hg19.test.vcf

inst/extdata/hg38.test.vcf

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man/COSMIC_hg19_demo.Rd man/COSMIC_hg38_demo.Rd man/ExamplePaneldesign.Rd man/ExampleWESdesign.Rd man/ExampleWESvcfs.Rd man/Hellman_SimulatedFM1Panel_WES.Rd man/HumanTumorSuppressors.Rd man/TMB_Horizon.Rd man/TMB_VanAllen.Rd man/TMBs_SimulatedPanel.Rd man/TMBs_WES.Rd man/VanAllen_Clinical.Rd man/annotateTMB.Rd man/applyFilters.Rd man/applySimulatePanel.Rd man/applyTMB.Rd man/callFilters.Rd man/callTMB.Rd man/compareROC.Rd man/compareTMBdistribution.Rd man/correlateTMBvalues.Rd man/dot-fetch_filtered_SNV.Rd man/dot-remove_noncoding_SNV.Rd man/filterByVAF.Rd man/filterCOSMIC.Rd man/filterTruncatingTumorSuppr.Rd man/filterVariantType.Rd man/formatCOSMIC.Rd man/generateBoxplot.Rd man/generateROC.Rd man/inputToTMB.Rd man/plotTMB.Rd man/readDesign.Rd man/readVcfFiles.Rd man/removeCancerVariants.Rd man/simulatePanel.Rd man/vcfs_NoCancer_ForPanel.Rd man/vcfs_all.Rd

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tests/testthat.R

tests/testthat/example_panel.bed

vignettes/vignettes.Rproj

vignettes/workflow_tmbtool_p1.png

acc-bioinfo/TMBleR documentation built on Dec. 18, 2021, 10:21 p.m.

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acc-bioinfo/TMBleR
Tumor Mutational Burden Quantification From Gene Panels And WES

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Tumor Mutational Burden Quantification From Gene Panels And WES

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acc-bioinfo/TMBleR Tumor Mutational Burden Quantification From Gene Panels And WES

Files in acc-bioinfo/TMBleR Tumor Mutational Burden Quantification From Gene Panels And WES

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acc-bioinfo/TMBleR
Tumor Mutational Burden Quantification From Gene Panels And WES

Files in acc-bioinfo/TMBleR
Tumor Mutational Burden Quantification From Gene Panels And WES