zavolanlab / CFI2021

Supplementary Materials

CFI 2021

Traverse to the desired path in your file system, then clone the repository and move into it with:

git clone https://github.com/zavolanlab/CFI2021.git
cd CFI2021

Different analyses are described in different directories:

• Exact commands related to RNA-Seq data processing are described in Preprocessing/README.md.

• Reproducing the differential gene expression analyses is described in Differential_Gene_Expression_Analysis/README.md.

• Information on creating coverage profile plots were collected in Coverage_Plots/plot-coverages.R.

• All the analyses related to transcripts' 3' ends are gathered in the following notebook: Terminal_Exons_Analysis/report.ipynb.

  Please follow the code there to reproduce plots presented in Fig. 1.

• Scripts for running KSEA analysis are located in the folder KSEA_Phospho_Proteomics_Analysis.

• To reproduce Fig. S3, run the following R script:

  Rscript Figure_S3/CDFs_proteomics_transcriptomics_targets.R

  Files with panels of Fig. S3 Figure_S3/Cumulative_distribution_proteomics_targets_nontargets.pdf and Figure_S3/Cumulative_distribution_transcriptomics_targets_nontargets.pdf will be generated.