/CTAT_VIF_Paper

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CTAT_VIF_Paper

  • CTAT-VIF accuracy with simulated reads for virus integrations:

    • 0.characterizing_VIF_accuracy_wSIM_data/uniform_coverage_virus_detection/PE/sim50_PE

  • Benchmarking CTAT-VIF in comparison to related methods using simulated data:

    • 1.Benchmarking_available_tools/bmark_sim50/examine_bmark_accuracy.by_replicate.Rmd

  • Reanalysis of NatGenetics 2015 Hu et al.

    • 2.NatGenetics2015_reanalysis/NatGenetics2015_VIF/compare_VIF_vs_published_insertions/compare_VIF_to_published_NatGenet2015.Rmd

    • 2.NatGenetics2015_reanalysis/NatGenetics2015_VIF/compare_VIF_vs_published_insertions/compare_VIF_to_published_NatGenet2015.SangerValidated.Rmd

  • Virus Content Detected Across Diverse Tumor and Normal Tissues

    • 4.Combined_VIF_analysis/SampleCounting.Rmd: Using CTAT-VIF, we surveyed virus content and integrations across 33,762 samples involving 13,773 study participants or cell lines. (Table: all_samples_processed.tsv)

    • 4.Combined_VIF_analysis/VirusContentAnalysis/VirusContentAnalysis.Rmd (Table: virus_content_unfiltered.tsv)

  • CTAT-VIF Integration Data Quality Assessment and Filtering Potential Contaminants

    • 4.Combined_VIF_analysis/InsertionAnalysis/Insertion_threshold_analysis.VirusContentDisparity.Rmd

    • 4.Combined_VIF_analysis/InsertionAnalysis/Shared_Insertion_Sites.Rmd

    • 4.Combined_VIF_analysis/InsertionAnalysis/InsertionCounting.OrthogonalValidations.Rmd

    • 4.Combined_VIF_analysis/InsertionAnalysis/Insertion_threshold_analysis.by_orthogonal_brkpt_support.Rmd

  • Diverse viruses detected as genome insertions across tumor and normal tissues

    • 4.Combined_VIF_analysis/InsertionAnalysis/InsertionCounting.Rmd

  • Functional impacts of insertions

    • 4.Combined_VIF_analysis/Insertion_and_CNVs/Insertions_and_CNVs.Rmd

    • 4.Combined_VIF_analysis/Insertion_and_EXPR_effects/InsertionExpressionEffects.Rmd

    • 4.Combined_VIF_analysis/Insertion_STARF_Fusion_Mapping/InsertionFusionMappingCurrentFusionInspector.Rmd

    • 4.Combined_VIF_analysis/Insertion_Spliced_Human/InsertionToGeneAndSplice.Rmd

  • Insertion Hotspots

    • 4.Combined_VIF_analysis/InsertionHotspots

      • run_hotspots.sh - computes insertion hotspots.

      • then DecorateInsertions/DecorateInsertions.Rmd - Table

    • 4.Combined_VIF_analysis/InsertionHotspots/AnalyzeHotspotSizes.Rmd : Figure 6b

    • 4.Combined_VIF_analysis/InsertionHotspots/HotspotRandomness.Rmd : Figure 6a

    • 4.Combined_VIF_analysis/InsertionHotspots/AnalyzeTopHotspots.Rmd : Figure 6c

    • 4.Combined_VIF_analysis/InsertionHotspots/ExploreHotspots/ : Figure 7

    • 4.Combined_VIF_analysis/InsertionHotspots/HotspotVirusCancerRepresentation.Rmd

    • 4.Combined_VIF_analysis/InsertionHotspots/TopHotspotsByVirusType.Rmd