Files in parklab/SigMA

Signature Multivariate Analysis

.travis.yml

DESCRIPTION

LICENSE

NAMESPACE

R/assignment.R R/calc_cos.R R/calc_llh.R R/combine_SBS_indel.R R/decompose.R R/find_data_setting.R R/get_trinuc_norm.R R/list_options.R R/lite_df.R R/make_matrix.R R/match_to_catalog.R R/mmej_nhej_indels_from_vcfs.R R/overlap_repeats.R R/plot_detailed.R R/plot_summary.R R/plot_tribase_dist.R R/predict_mmrd.R R/predict_mva.R R/quick_simulation.R R/run.R R/run_overlap_repeats.R

R/sysdata.rda

R/tune_new_gbm.R R/utils.R README.md

SigMA.Rproj

build-docker-image.sh

docker-context/Dockerfile

docker-context/README.md examples/convert_muts_to_bed.R examples/create_list_bedfiles.R examples/example_combine_files_mmrd.R examples/example_find_settings.R

examples/example_mmrd_SBS_matrix.csv

examples/example_msisensor_file.csv

examples/example_muts_mmrd.maf

examples/make_snv_id_input_HRD.R examples/make_table_indel_repeat.R

examples/overlap_with_repeat_regions.sh

examples/pull_bed_files_from_lfs.sh

examples/run_SigMA_MMRD.R

examples/tcga_mc3_brca.maf

examples/test.R examples/test_determine_cutoff.R examples/test_estimate_exposures_by_matching_to_WGS_simul.R examples/test_maf.R

examples/test_mutations_50sample.maf

examples/test_tune_example.R examples/test_tune_example_forPfizer.R

inst/extdata/examples/example_small_bedfile.bed

inst/extdata/examples/msk_impact_2017_clinical_data_selected_Oncotree_Codes.tsv

inst/extdata/examples/seqcap_capture.bed

inst/extdata/examples/tcga_mc3_brca.maf

inst/extdata/examples/test_mutations_50sample.maf

inst/extdata/gbm_models/README.txt

inst/extdata/matrices/matrices_96dim.rda

inst/extdata/repeat_bed_files/.gitattributes

inst/extdata/repeat_bed_files/merged_bed_10to13.bed

inst/extdata/repeat_bed_files/merged_bed_1_14to16.bed

inst/extdata/repeat_bed_files/merged_bed_2to3.bed

inst/extdata/repeat_bed_files/merged_bed_4_XtoY.bed

inst/extdata/repeat_bed_files/merged_bed_5_17to_22.bed

inst/extdata/repeat_bed_files/merged_bed_6to9.bed

inst/extdata/vcf_examples/0448206f-3ade-4087-b1a9-4fb2d14e1367.vcf

inst/extdata/vcf_examples/ddc7377d-82c3-480a-be3c-3d1da52c77d4.consensus.snv_mnv.vcf

install.R man/assignment.Rd man/calc_llh.Rd man/cosine.Rd man/decompose.Rd man/lite_df.Rd man/make_matrix.Rd man/match_to_catalog.Rd man/plot_detailed.Rd man/plot_summary.Rd man/plot_tribase_dist.Rd man/predict_mva.Rd man/run.Rd manual_sigma.pdf runShiny.R shiny/server.R shiny/ui.R

shiny/www/howtorun.png

shiny/www/sigma.jpg

shiny/www/workflow.png

parklab/SigMA documentation built on Feb. 10, 2024, 6:59 p.m.