steverozen/PCAWG7
Repository of Data from paper 'The repertoire of Mutational Signatures in Human Cancer'

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steverozen/PCAWG7: Repository of Data from paper 'The repertoire of Mutational Signatures in Human Cancer'
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Files in steverozen/PCAWG7
Repository of Data from paper 'The repertoire of Mutational Signatures in Human Cancer'

.Rbuildignore
.github/.gitignore
.github/workflows/check-standard.yaml
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
PCAWG7.Rproj
R/CancerTypes.R R/PCAWG7.R R/SampleIDToCancerType.R R/SignatureExposureInfo.R R/SplitMatrixBySampleType.R R/SplitPCAWGMatrixByTumorType.R R/TCGA_ID_to_ICGC_ID.R R/data.R R/map_SP_ID_to_tumor_type.R R/map_aliquot_ID_to_SP_ID.R
R/sysdata.rda
README.md README.rmd cran-comments.md
data-raw/ED.table.1.csv
data-raw/PCAWG7_0.1.3.pdf data-raw/boxplot.idea.R
data-raw/cosSim2.csv
data-raw/generate_package_data.R data-raw/load.PCAWG.sample.sheets.R data-raw/old.code/SignatureExposureInfo.R data-raw/old.code/SplitMatrixByTumorType.R data-raw/package-data-related/code/convert-tcga_id-to-icgc_specimen_id.R data-raw/package-data-related/code/generate-PCAWG-sample-sheet.R data-raw/package-data-related/code/generate-package-internal-data.R
data-raw/package-data-related/source-files/COSMIC-v3-DBS-proposed-aetiology-short-form.csv
data-raw/package-data-related/source-files/COSMIC-v3-ID-proposed-aetiology-short-form.csv
data-raw/package-data-related/source-files/COSMIC-v3.2-SBS-proposed-aetiology-short-form.csv
data-raw/pcawg.sample.sheets/pc_annotation-tcga_uuid2barcode.tsv.gz
data-raw/pcawg.sample.sheets/pcawg_sample_sheet.2016-06-24.blacklisted_donors.tsv
data-raw/pcawg.sample.sheets/pcawg_sample_sheet.v1.4.2016-09-14.tsv
data-raw/pcawg.sample.sheets/release_may2016.v1.4.tsv
data-raw/pcawg.sample.sheets/release_may2016.v1.4.with_consensus_calls.tsv
data-raw/plots/PCAWG7.DBS78.count.sigs.pdf data-raw/plots/PCAWG7.DBS78.density.sigs.pdf data-raw/plots/PCAWG7.ID.count.sigs.pdf data-raw/plots/PCAWG7.SBS192.count.sigs.pdf data-raw/plots/PCAWG7.SBS192.density.sigs.pdf data-raw/plots/PCAWG7.SBS96.count.sigs.pdf data-raw/plots/PCAWG7.SBS96.density.sigs.pdf data-raw/plots/PCAWG7SBS96.flat.pdf data-raw/plots/all.dbs.spectra.pdf data-raw/plots/no.lung.no.skin.no.liver.pdf data-raw/plots/no.lung.no.skin.pdf
data-raw/sig.profiler.exposures/PCAWG_SigProfiler_ID_signatures_in_samples.csv
data-raw/sig.profiler.exposures/PCAWG_sigProfiler_DBS_signatures_in_samples.csv
data-raw/sig.profiler.exposures/PCAWG_sigProfiler_SBS_signatures_in_samples.csv
data-raw/sig.profiler.exposures/TCGA_WES_sigProfiler_ID_signatures_in_samples.csv
data-raw/sig.profiler.exposures/TCGA_WES_sigProfiler_SBS_signatures_in_samples.csv
data-raw/sig.profiler.exposures/load.package.variable.exposure.R
data-raw/sig.profiler.exposures/nonPCAWG_WES_sigProfiler_SBS_signatures_in_samples_2018_04_13.csv
data-raw/sig.profiler.exposures/nonPCAWG_WGS_sigProfiler_SBS_signatures_in_samples_2018_04_13.csv
data-raw/sig.profiler.signatures/populate.variable.signature.R
data-raw/sig.profiler.signatures/sigProfiler_DBS_signatures.csv
data-raw/sig.profiler.signatures/sigProfiler_ID_signatures.csv
data-raw/sig.profiler.signatures/sigProfiler_ID_signatures_fixed_rownames.csv
data-raw/sig.profiler.signatures/sigProfiler_SBS_signatures_2019_05_22.csv
data-raw/sig.profiler.signatures/sigProfiler_TSB_signatures.csv
data-raw/sig.profiler.signatures/sigProfiler_exome_SBS_signatures.csv
data-raw/spectra/WES_Other.1536.csv
data-raw/spectra/WES_Other.192.csv
data-raw/spectra/WES_Other.96.csv
data-raw/spectra/WES_Other.dinucs.csv
data-raw/spectra/WES_TCGA.1536.csv
data-raw/spectra/WES_TCGA.192.csv
data-raw/spectra/WES_TCGA.96.csv
data-raw/spectra/WES_TCGA.dinucs.csv
data-raw/spectra/WES_TCGA.indels.csv
data-raw/spectra/WGS_Other.1536.csv
data-raw/spectra/WGS_Other.192.csv
data-raw/spectra/WGS_Other.96.csv
data-raw/spectra/WGS_Other.dinucs.csv
data-raw/spectra/WGS_PCAWG.1536.csv
data-raw/spectra/WGS_PCAWG.192.csv
data-raw/spectra/WGS_PCAWG.96.csv
data-raw/spectra/WGS_PCAWG.dinucs.csv
data-raw/spectra/WGS_PCAWG.indels.csv
data-raw/spectra/load.package.variable.spectra.R data-raw/test-signature-attribution.R
data/PCAWG.sample.id.rda
data/PCAWG.sample.sheet.rda
data/exposure.rda
data/exposure.stats.rda
data/spectra.rda
demo/00Index
demo/extended.data.table.1.R
inst/WORDLIST
man/CancerTypes.Rd man/ExposureStats1TumorType.Rd man/PCAWG.sample.id.Rd man/PCAWG.sample.sheet.Rd man/PCAWG7.Rd man/SampleIDToCancerType.Rd man/SplitMatrixBySampleType.Rd man/SplitPCAWGMatrixByTumorType.Rd man/TCGA_ID_to_ICGC_ID.Rd man/exposure.Rd man/exposure.stats.Rd man/map_SP_ID_to_tumor_type.Rd man/map_aliquot_ID_to_SP_ID.Rd man/spectra.Rd news.md tests/testthat.R tests/testthat/test_SampleIDToCancerType.R tests/testthat/test_SplitMatrixBySampleType.R tests/testthat/test_SplitPCAWGMatrixByTumorType.R tests/testthat/test_TCGA_ID_to_ICGA_ID.R tests/testthat/test_map_aliquot_ID_to_SP_ID.R
steverozen/PCAWG7 documentation built on Feb. 2, 2022, 5:40 a.m.

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