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

File type	File
	MAJIQ_Modulizer_output_to_rds.R
	MAJIQ_AS_analysis.Rmd

File typ	File
	Dose_response_curve_fitting.Rmd

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

File type	File
	rG4_prediction.R
	Dependence_of_binding_and_cooperativity_on_rG4s.Rmd

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

File type	File
	in_vitro_CLIP_analysis.Rmd

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