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CTAT-VIF accuracy with simulated reads for virus integrations:
- 0.characterizing_VIF_accuracy_wSIM_data/uniform_coverage_virus_detection/PE/sim50_PE
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Benchmarking CTAT-VIF in comparison to related methods using simulated data:
- 1.Benchmarking_available_tools/bmark_sim50/examine_bmark_accuracy.by_replicate.Rmd
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Reanalysis of NatGenetics 2015 Hu et al.
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2.NatGenetics2015_reanalysis/NatGenetics2015_VIF/compare_VIF_vs_published_insertions/compare_VIF_to_published_NatGenet2015.Rmd
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2.NatGenetics2015_reanalysis/NatGenetics2015_VIF/compare_VIF_vs_published_insertions/compare_VIF_to_published_NatGenet2015.SangerValidated.Rmd
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Virus Content Detected Across Diverse Tumor and Normal Tissues
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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)
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4.Combined_VIF_analysis/VirusContentAnalysis/VirusContentAnalysis.Rmd (Table: virus_content_unfiltered.tsv)
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CTAT-VIF Integration Data Quality Assessment and Filtering Potential Contaminants
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4.Combined_VIF_analysis/InsertionAnalysis/Insertion_threshold_analysis.VirusContentDisparity.Rmd
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4.Combined_VIF_analysis/InsertionAnalysis/Shared_Insertion_Sites.Rmd
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4.Combined_VIF_analysis/InsertionAnalysis/InsertionCounting.OrthogonalValidations.Rmd
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4.Combined_VIF_analysis/InsertionAnalysis/Insertion_threshold_analysis.by_orthogonal_brkpt_support.Rmd
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Diverse viruses detected as genome insertions across tumor and normal tissues
- 4.Combined_VIF_analysis/InsertionAnalysis/InsertionCounting.Rmd
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Functional impacts of insertions
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4.Combined_VIF_analysis/Insertion_and_CNVs/Insertions_and_CNVs.Rmd
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4.Combined_VIF_analysis/Insertion_and_EXPR_effects/InsertionExpressionEffects.Rmd
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4.Combined_VIF_analysis/Insertion_STARF_Fusion_Mapping/InsertionFusionMappingCurrentFusionInspector.Rmd
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4.Combined_VIF_analysis/Insertion_Spliced_Human/InsertionToGeneAndSplice.Rmd
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Insertion Hotspots
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4.Combined_VIF_analysis/InsertionHotspots
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run_hotspots.sh - computes insertion hotspots.
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then DecorateInsertions/DecorateInsertions.Rmd - Table
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4.Combined_VIF_analysis/InsertionHotspots/AnalyzeHotspotSizes.Rmd : Figure 6b
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4.Combined_VIF_analysis/InsertionHotspots/HotspotRandomness.Rmd : Figure 6a
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4.Combined_VIF_analysis/InsertionHotspots/AnalyzeTopHotspots.Rmd : Figure 6c
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4.Combined_VIF_analysis/InsertionHotspots/ExploreHotspots/ : Figure 7
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4.Combined_VIF_analysis/InsertionHotspots/HotspotVirusCancerRepresentation.Rmd
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4.Combined_VIF_analysis/InsertionHotspots/TopHotspotsByVirusType.Rmd
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