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Tretow_et_al_2023

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.

1_Quality_assessment

File type File
Quality_assessment.Rmd

2_MAJIQ_AS_analysis

File type File
MAJIQ_Modulizer_output_to_rds.R
MAJIQ_AS_analysis.Rmd

3_Dose_response_curve_fitting

File typ File
Dose_response_curve_fitting.Rmd

4_iCLIP_analysis

File type File
Binding_site_definition.R
Create_CE_minigenes.R
Calculate_TPMs_in_Controls.R
Genomic_location_of_binding_sites.Rmd
Sequence_composition_of_binding_sites.Rmd
RNAmaps_of_regulated_events.Rmd

5_rG4_analysis

File type File
rG4_prediction.R
Dependence_of_binding_and_cooperativity_on_rG4s.Rmd

6_RTstop profiling

File type File
rG4_prediction_on_in_vitro_library_constructs.R
Summary_of_the_in_vitro_library.Rmd
Comparison_RTstop_profiling_and_predictions.Rmd

7_ivCLIP

File type File
in_vitro_CLIP_analysis.Rmd

8_TCGA_analysis

File type File
Calculate_expression_BRCA.R
Create_GRanges_object_with_junctions_of_interest.R
Calculate_PSIs_BRCA.R
Calculate_adjusted_Rand_Indices.R
Correlation_HNRNPH_levels_and_splicing_events.Rmd
Clustering_BRCA_samples.Rmd

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