Files in campbio/BAGEL
Novel Mutational Signature Analysis
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md
R/annotate_variants.R
R/cosmic_data.R
R/discovery_prediction.R
R/load_data.R
R/main_class.R
R/plotting.R
R/standard_tables.R
R/sysdata.rda
R/table_utils.R
R/utils-pipe.R
README.md
codecov.yml
data-raw/cosmic_signatures.txt
data-raw/create_cosmicResult.R
data-raw/sigProfiler_DBS_signatures.csv
data-raw/sigProfiler_ID_signatures.csv
data-raw/sigProfiler_SBS_signatures_2019_05_22.csv
data-raw/sigProfiler_exome_SBS_signatures.csv
data/cosmic_v2_sigs.rda
data/cosmic_v3_dbs_sigs.rda
data/cosmic_v3_indel_sigs.rda
data/cosmic_v3_sbs_sigs.rda
data/cosmic_v3_sbs_sigs_exome.rda
data/rep_range.rda
inst/testdata/bagel.rds
inst/testdata/bagel_annot.rds
inst/testdata/bagel_sbs96.rds
inst/testdata/bagel_sbs96_tiny.rds
inst/testdata/dbs_bagel.rds
inst/testdata/dt.rds
inst/testdata/incomplete-bagel.rds
inst/testdata/indel_bagel.rds
inst/testdata/public_LUAD_TCGA-97-7938.vcf
inst/testdata/public_LUAD_TCGA-MP-A4TJ.vcf
inst/testdata/public_SKCM_TCGA-EE-A3J5-06A-11D-A20D-08.vcf
inst/testdata/public_SKCM_TCGA-ER-A197-06A-32D-A197-08.vcf
inst/testdata/public_SKCM_TCGA-ER-A19O-06A-11D-A197-08.vcf
inst/testdata/public_TCGA.LUSC.maf
inst/testdata/res.rds
inst/testdata/res_annot.rds
inst/testdata/res_annot_umap.rds
inst/testdata/sample_annotations.txt
inst/testdata/test_res.rds
man/Result-class.Rd
man/Result_Grid-class.Rd
man/add_flank_to_variants.Rd
man/add_sample_annotations.Rd
man/add_variant_type.Rd
man/annotate_replication_strand.Rd
man/annotate_transcript_strand.Rd
man/annotate_variant_length.Rd
man/annotate_variant_type.Rd
man/auto_predict_grid.Rd
man/auto_subset_sigs.Rd
man/bagel-class.Rd
man/build_custom_table.Rd
man/build_standard_table.Rd
man/combine_predict_grid.Rd
man/compare_cosmic_v2.Rd
man/compare_cosmic_v3.Rd
man/compare_results.Rd
man/cosmic_v2_sigs.Rd
man/cosmic_v2_subtype_map.Rd
man/cosmic_v3_dbs_sigs.Rd
man/cosmic_v3_indel_sigs.Rd
man/cosmic_v3_sbs_sigs.Rd
man/cosmic_v3_sbs_sigs_exome.Rd
man/count_table-class.Rd
man/create_bagel.Rd
man/create_dbs_table.Rd
man/create_sbs192_table.Rd
man/create_sbs96_table.Rd
man/create_umap.Rd
man/discover_signatures.Rd
man/drop_annotation.Rd
man/extract_count_tables.Rd
man/extract_variants.Rd
man/extract_variants_from_maf.Rd
man/extract_variants_from_maf_file.Rd
man/extract_variants_from_matrix.Rd
man/extract_variants_from_vcf.Rd
man/extract_variants_from_vcf_file.Rd
man/generate_result_grid.Rd
man/get_sample_annotations.Rd
man/get_sample_names.Rd
man/get_variants.Rd
man/init_sample_annotations.Rd
man/jsd.Rd
man/name_signatures.Rd
man/pipe.Rd
man/plot_exposures.Rd
man/plot_exposures_by_annotation.Rd
man/plot_full.Rd
man/plot_sample_counts.Rd
man/plot_sample_reconstruction_error.Rd
man/plot_signatures.Rd
man/plot_umap.Rd
man/plot_umap_sigs.Rd
man/predict_exposure.Rd
man/rc.Rd
man/rep_range.Rd
man/select_genome.Rd
man/set_sample_annotations.Rd
man/subset_bagel_by_annotation.Rd
man/subset_bagel_by_counts.Rd
man/subset_variant_by_type.Rd
man/subset_variants_by_samples.Rd
man/table_96.Rd
tests/testthat.R
tests/testthat/test-load-vcf.R
tests/testthat/test-plotting.R
tests/testthat/test-signatures.R
vignettes/.gitignore
vignettes/bagel.Rmd
vignettes/bagel.pdf
