zarnackgroup/prieto_garcia_et_al_2023

Fork of original repository for group storage

Prieto_Garcia_et_al_2023

In this repository the R-Scrips and Rmarkdown reports of Prieto-Garcia et al. 2024 are provided.

R-Scripts and Rmarkdown reports have to be executed in the following order:

• 01_modulizer_output_to_rds.R
• 02_effect_of_USP39_KD_on_splicing.Rmd
• 03_get_read_support_for_A5SS_events.R
• 04_generate_peptide_and_adjusted_SWISSPROT_sequences.Rmd
• 05_adjust_IDs_for_FAS_analysis.R
• 06_FASscore_analysis.Rmd

These first rendered HTML-Reports can be accessed at https://mchicken1988.github.io/Prieto_Garcia_et_al_2023/

figure 1 and s4 code

• 07_modulize_to_regulated_granges_rds.R
• 08_modulize_to_unregulated_granges_rds.R
• 09_modulize_to_regulated_a5ss_rds.R
• 10_figures_1_s4_garcia_et_al_2024

the commands for the splicing analysis can be found in

• 11_majiq_porcession.Rmd