Files in luannnguyen/CHORD
Classifier of Homologous Recombination Deficiency
DESCRIPTION
LICENSE
NAMESPACE
R/chordPredict.R
R/dataChord.R
R/extractSigsChord.R
README.md
data/CHORD.rda
example/README.Rmd
example/output/chord_pred.txt
example/output/contexts/PD10010_contexts.txt
example/output/contexts/PD11352_contexts.txt
example/output/contexts/PD3905_contexts.txt
example/output/contexts/PD4116_contexts.txt
example/output/contexts/PD7344_contexts.txt
example/output/merged_contexts.txt
example/vcf/PD10010_snv_indel.vcf.gz
example/vcf/PD10010_sv.vcf.gz
example/vcf/PD11352_snv_indel.vcf.gz
example/vcf/PD11352_sv.vcf.gz
example/vcf/PD3905_snv_indel.vcf.gz
example/vcf/PD3905_sv.vcf.gz
example/vcf/PD4116_snv_indel.vcf.gz
example/vcf/PD4116_sv.vcf.gz
example/vcf/PD7344_snv_indel.vcf.gz
example/vcf/PD7344_sv.vcf.gz
man/CHORD.Rd
man/chordPredict.Rd
man/extractSigsChord.Rd
paper/extract_features/HMF_DR010_DR047/annotate_genes/annotate_genes.sh
paper/extract_features/HMF_DR010_DR047/annotate_genes/detGeneStatuses_exec.R
paper/extract_features/HMF_DR010_DR047/annotate_genes/merge_diplotypes.sh
paper/extract_features/HMF_DR010_DR047/extract_sigs/extract_sigs.R
paper/extract_features/HMF_DR010_DR047/extract_sigs/extract_sigs.sh
paper/extract_features/HMF_DR010_DR047/extract_sigs/merge_sig_vectors.R
paper/extract_features/HMF_DR010_DR047/extract_sigs/merge_sig_vectors.sh
paper/extract_features/PCAWG_2020/annotate_genes/annotate_genes.sh
paper/extract_features/PCAWG_2020/annotate_genes/detGeneStatuses_exec.R
paper/extract_features/PCAWG_2020/annotate_genes/merge_diplotypes.sh
paper/extract_features/PCAWG_2020/annotate_genes/mk_manifest.R
paper/extract_features/PCAWG_2020/extract_sigs/extract_sigs.R
paper/extract_features/PCAWG_2020/extract_sigs/extract_sigs.sh
paper/extract_features/PCAWG_2020/extract_sigs/merge_sig_vectors.R
paper/extract_features/PCAWG_2020/extract_sigs/merge_sig_vectors.sh
paper/misc/cluster_features.R
paper/misc/cn_loss_enrichment_2.R
paper/misc/downscale_mut_perf.R
paper/misc/find_novel_vus.R
paper/misc/impact_of_msi_on_chord.R
paper/misc/radiotherapy_features.R
paper/pancancer_analysis/det_hr_genes.R
paper/pancancer_analysis/det_hrd_cause.R
paper/pancancer_analysis/hrd_by_cancer_type.R
paper/performance/chord_v1_vs_v2.R
paper/performance/summarize_perf.R
training/ct_holdout/do_ct_holdout_training.R
training/ct_holdout/perf_ct_holdout.R
training/sel_training_samples/sel_training_samples_HMF_DR010_DR047.R
training/sel_training_samples/sel_training_samples_PCAWG_2020.R
training/train_pipeline/doCvSelSamples.R
training/train_pipeline/spawnOuterCvData.R
training/train_pipeline/trainCoreFunctions.R
training/train_pipeline/trainFinalOnWhitelist.R
training/train_pipeline/trainPipeline.sh
