This repository comprises all R-scripts and Rmarkdown files used to generate the results and plots in Tretow et al. 2023.
The analyses are divided into 8 sections. The sections and the R scripts and Rmarkdown files within the sections must be run in the order given.
The rendered HTML-Reports can be accessed via the project's GitHub Page.
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Quality_assessment.Rmd |
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MAJIQ_Modulizer_output_to_rds.R |
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MAJIQ_AS_analysis.Rmd |
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Dose_response_curve_fitting.Rmd |
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Binding_site_definition.R |
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Create_CE_minigenes.R |
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Calculate_TPMs_in_Controls.R |
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Genomic_location_of_binding_sites.Rmd |
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Sequence_composition_of_binding_sites.Rmd |
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RNAmaps_of_regulated_events.Rmd |
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|---|---|
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rG4_prediction.R |
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Dependence_of_binding_and_cooperativity_on_rG4s.Rmd |
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|---|---|
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rG4_prediction_on_in_vitro_library_constructs.R |
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Summary_of_the_in_vitro_library.Rmd |
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Comparison_RTstop_profiling_and_predictions.Rmd |
| File type | File |
|---|---|
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in_vitro_CLIP_analysis.Rmd |
| File type | File |
|---|---|
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Calculate_expression_BRCA.R |
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Create_GRanges_object_with_junctions_of_interest.R |
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Calculate_PSIs_BRCA.R |
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Calculate_adjusted_Rand_Indices.R |
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Correlation_HNRNPH_levels_and_splicing_events.Rmd |
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Clustering_BRCA_samples.Rmd |