Files in steverozen/ICAMSxtra
ICAMSxtra
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.gitignore
DESCRIPTION
ICAMSxtra.Rproj
ICAMSxtra_0.1.0.pdf
NAMESPACE
NEWS.md
R/ID115_fns.R
R/ID_fns.R
R/TP_FP_FN_avg_sim.R
R/data.R
R/exposure_related_functions.R
R/internal_matches.R
R/match.sigs.R
R/match_two_sig_sets.R
R/plot_error_bar_fns.R
R/sig_dist_matrix.R
R/sysdata.rda
README.Rmd
README.md
appveyor.yml
data-raw/create_catalog_row_headers_ID115.R
data-raw/create_catalogs_ID115.R
data-raw/create_spectra_from_vcfs.R
data-raw/create_testdata_for_AnnotateIDVCFsWithTransRanges.R
data-raw/create_trans_proportions.R
data-raw/jia.geng.notes.txt
data-raw/save_global_variables.R
data-raw/source-file/ICAMSxtra_0.0.4.9006.tar.gz
data-raw/source-file/ICAMSxtra_0.0.5.tar.gz
data-raw/vcfs/HepG2_Cis/HepG2_Cis_cl1.vcf.gz
data-raw/vcfs/HepG2_Cis/HepG2_Cis_cl2.vcf.gz
data-raw/vcfs/HepG2_Cis/HepG2_Cis_cl3.vcf.gz
data-raw/vcfs/HepG2_Cis/HepG2_Cis_cl4.vcf.gz
data-raw/vcfs/MCF10A_Cis/MCF10A_Cis_cl1.vcf.gz
data-raw/vcfs/MCF10A_Cis/MCF10A_Cis_cl2.vcf.gz
data-raw/vcfs/MCF10A_Cis/MCF10A_Cis_cl3.vcf.gz
data-raw/vcfs/MCF10A_Cis/MCF10A_Cis_cl4.vcf.gz
data-raw/vcfs/MCF10A_Cis/MCF10A_Cis_cl5.vcf.gz
data-raw/vcfs/MCF10A_Cis/MCF10A_Cis_cl6.vcf.gz
data/GRCh37.proportions.rda
data/GRCh38.proportions.rda
data/catalog.row.order.rda
data/reverse.rda
data/reverse_pooled.rda
data/target.rda
data/target_pooled.rda
docs/index.html
docs/src/contrib/ICAMSxtra_0.0.6.tar.gz
docs/src/contrib/PACKAGES
docs/src/contrib/PACKAGES.gz
docs/src/contrib/PACKAGES.rds
inst/WORDLIST
inst/extdata/103894.annotated.rda
inst/extdata/Strelka-ID-vcf/Strelka.ID.GRCh37.s1.vcf
inst/extdata/Strelka-ID-vcf/Strelka.ID.GRCh37.s2.vcf
inst/extdata/annotated.ID.vcf.rda
inst/extdata/annotated.ID4a.samples.PCAWG.rda
inst/extdata/synthetic.exposure.csv
man/AnnotateIDVCFsWithTransRanges.Rd
man/Canonicalize1Del115.Rd
man/Canonicalize1ID115.Rd
man/Canonicalize1INS115.Rd
man/CanonicalizeID115.Rd
man/CatalogRowOrder.Rd
man/Collapse115CatalogTo83.Rd
man/CollapseID115CatalogsToID83s.Rd
man/CreateOneColID115Matrix.Rd
man/GRCh37.proportions.Rd
man/GRCh38.proportions.Rd
man/Match1Sig.Rd
man/MatchSigs1Direction.Rd
man/MatchSigs2Directions.Rd
man/MatchSigsAndRelabel.Rd
man/MeanOfSpectraAsSig.Rd
man/NumFromId.Rd
man/PlotExposure.Rd
man/PlotExposureInternal.Rd
man/PlotExposureToPdf.Rd
man/PlotID115AsID83ToPdf.Rd
man/PlotID115Catalog.Rd
man/PlotID115CatalogToPdf.Rd
man/PlotSpectraAsSigsWithUncertainty.Rd
man/PlotTransBiasID115.Rd
man/PlotTransBiasID115ToPdf.Rd
man/PlotTranscriptionAssociatedDamageToPdf.Rd
man/ReadExposure.Rd
man/ReadID115Catalog.Rd
man/Reverse.Rd
man/Reverse_pooled.Rd
man/SortExposure.Rd
man/TP_FP_FN_avg_sim.Rd
man/Target.Rd
man/Target_pooled.Rd
man/VCFsToID115Catalogs.Rd
man/VCFsToID115CatalogsAndPlotToPdf.Rd
man/WriteExposure.Rd
man/WriteID115Catalog.Rd
man/as.catalog.for.ID115.Rd
man/match_two_sig_sets.Rd
man/sig_dist_matrix.Rd
tests/testthat.R
tests/testthat/Rplots.pdf
tests/testthat/disconnected_test_AnnotateIDVCFsWithTransRanges.R
tests/testthat/match_two_sig_sets.R
tests/testthat/pdfs-for-comparison-ID115/PlotCatID115.counts.signature.test.pdf
tests/testthat/pdfs-for-comparison-ID115/PlotCatID115.counts.test.pdf
tests/testthat/test_ID_115_fns.R
tests/testthat/test_PlotID115Catalog.R
tests/testthat/test_PlotID115CatalogToPdf.R
tests/testthat/test_TP_FP_FN_avg_sim.R
tests/testthat/test_exposure_related_functions.R
tests/testthat/test_internal_matches.R
tests/testthat/test_match_two_sig_sets.R
tests/testthat/test_matchsigs.R
tests/testthat/test_plot_error_bar_fns.R
tests/testthat/test_sig_dist_matrix.R
tests/testthat/testdata/HepG2_Cis.spectra.csv
tests/testthat/testdata/HepG2_Duo_250pM_2mth_cl2_INDELintersect.vcf
tests/testthat/testdata/HepG2_Duo_250pM_2mth_cl3_INDELintersect.vcf
tests/testthat/testdata/MCF10A_Cis.spectra.csv
tests/testthat/testdata/Strelka-ID-GRCh37/Strelka.ID.GRCh37.s2.vcf
tests/testthat/testdata/Strelka-ID-GRCh37/Strelka.ID.GRCh37.vcf
tests/testthat/testdata/Strelka.ID.GRCh38.vcf
tests/testthat/testdata/create_one_col_delete_test_ID115.Rdata
tests/testthat/testdata/create_one_col_insert_test_ID115.Rdata
tests/testthat/testdata/synthetic.exposure.csv
tests/testthat/testdata/test_AnnotateIDVCFsWithTransRanges.Rdata
tests/testthat/testdata/test_AnnotateIDVCFsWithTransRanges.old.Rdata
tests/testthat/testdata/tiny.exposure.csv
tests/testthat/testdata/tiny.exposure.dup.csv
