├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── ImmuneLens_software_EULA_NC260523.docx ├── LICENSE ├── NAMESPACE ├── R ├── GCcorrect_WGS.R ├── IGH_gc_correct.R ├── IGH_haplotype_norm_for_region_diploid.R ├── IGH_haplotype_norm_for_region_tumour.R ├── IGH_haplotype_norm_fun.R ├── IGH_haplotype_norm_fun_tumour.R ├── IGH_somatic_norm_for_region.R ├── ImmuneLENS-package.R ├── ImmuneLENS.R ├── adjustImmuneLENS.R ├── baselineAdj.R ├── calcJSD_distance.R ├── calc_haplotype_regions_de_novo_diploid.R ├── calc_haplotype_regions_de_novo_highBcell.R ├── data.R ├── exonsImmuneLENS.R ├── exonwindowplot2.R ├── getCovFromBam_WGS.R ├── getLogRdf.R ├── getVDJFraction_ImmuneLENS.R ├── loadCov.R ├── medianExonCoverage.R ├── medianFilter.R ├── plotImmuneLENS.R ├── plotSegmentBubble.R ├── runImmuneLENS.R ├── run_somatic_correction_test.R ├── slidingwindowplot_alt.R ├── somatic_cna_IGH_caller.R ├── summariseWGS.R ├── sysdata.rda └── utils-pipe.R ├── README.md ├── data ├── TCRA_exons_agilent_v2_hg19.rda ├── TCRA_exons_agilent_v2_hg38.rda ├── TCRA_exons_hg19.rda ├── TCRA_exons_hg38.rda ├── TCRA_exons_nimblegen_hg19.rda ├── TCRA_exons_nimblegen_hg38.rda ├── TCRA_fasta.rda ├── TCRA_segments.rda ├── all_fasta.rda ├── all_fasta_hg38.rda ├── cov_example.rda ├── tcra_seg_hg19.rda ├── tcra_seg_hg19_vdj_version.rda ├── tcra_seg_hg38.rda ├── tcra_seg_hg38_vdj_version.rda ├── vdj.segments.list.rda └── vdj_seg_list.rda └── man ├── GCcorrect_WGS.Rd ├── IGH_gc_correct.Rd ├── IGH_haplotype_norm_for_region_diploid.Rd ├── IGH_haplotype_norm_fun.Rd ├── IGH_haplotype_norm_fun_tumour.Rd ├── IGH_somatic_norm_for_region.Rd ├── ImmuneLENS-package.Rd ├── TCRA_exons_agilent_v2_hg19.Rd ├── TCRA_exons_agilent_v2_hg38.Rd ├── TCRA_exons_hg19.Rd ├── TCRA_exons_hg38.Rd ├── TCRA_exons_nimblegen_hg19.Rd ├── TCRA_exons_nimblegen_hg38.Rd ├── TCRA_fasta.Rd ├── TCRA_segments.Rd ├── adjustImmuneLENS.Rd ├── all_fasta.Rd ├── all_fasta_hg38.Rd ├── baselineAdj.Rd ├── calcJSD_distance.Rd ├── calc_haplotype_regions_de_novo_diploid.Rd ├── calc_haplotype_regions_de_novo_highBcell.Rd ├── cov_example.Rd ├── exonsImmuneLENS.Rd ├── exonwindowplot2.Rd ├── getCovFromBam_WGS.Rd ├── getLogRdf.Rd ├── getVDJfraction_ImmuneLENS.Rd ├── loadCov.Rd ├── medianExonCoverage.Rd ├── medianFilter.Rd ├── pipe.Rd ├── plotImmuneLENS.Rd ├── plotSegmentBubble.Rd ├── runImmuneLENS.Rd ├── run_somatic_correction_test.Rd ├── slidingwindowplot_alt.Rd ├── somatic_cna_IGH_caller.Rd ├── summariseWGS.Rd ├── tcra_seg_hg19.Rd ├── tcra_seg_hg19_vdj.Rd ├── tcra_seg_hg38.Rd ├── tcra_seg_hg38_vdj.Rd ├── vdj.segments.list.Rd └── vdj_seg_list.Rd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/McGranahanLab/ImmuneLENS/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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