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README.Rmd
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README.Rmd
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---
# date: "`r Sys.Date()`"
output: github_document
header-includes:
- \usepackage{amsfonts,amsmath,amsthm,amsbsy,amssymb,dsfont,bm,mathtools,mathalfa}
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# Code for SURF Analysis of ENCODE Data
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<!-- [](https://www.tidyverse.org/lifecycle/#experimental) -->
[](https://zenodo.org/badge/latestdoi/260113226)
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This repository makes available the source code for our SURF paper(s). Last updated in April 2020.
The paper presents the **S**tatistical **U**tility for **R**BP **F**unctions (SURF) for integrative analysis of RNA-seq and CLIP-seq data. The goal of SURF is to identify alternative splicing (AS), alternative transcription initiation (ATI), and alternative polyadenylation (APA) events regulated by individual RBPs and elucidate protein-RNA interactions governing these events. We apply the SURF pipeline to analyze 104 RBP data sets (from [ENCODE](https://www.encodeproject.org)). Check out the browsable results from this [shiny](http://www.statlab.wisc.edu/shiny/surf/) app!
The current repository includes:
* application/
* `xena.R`: process TCGA and GTEx transcriptome data.
* `encode_surf_one.R`: perform SURF analysis for one RBP. This is used for all 104 RBPs.
* `encode_surf_summary.R`: summarize the SURF results, including all the statistics and plots reported in the paper.
* simulation/
* `other_simulation.sh`: prepare DEXSeq and run [rMATS](http://rnaseq-mats.sourceforge.net/) and [MAJIQ](https://majiq.biociphers.org).
* `drseq_simulation.R`: run DrSeq and DEXSeq, analyze simulation results, including all the statistics and plots reported in the paper.
* majiq/: contain two files needed for running MAJIQ.
* dexseq/: contain two files needed for DEXSeq preparation.
To reproduce the ENCODE data analysis/results (available at (DOI): [10.5281/zenodo.3779037](https://doi.org/10.5281/zenodo.3779037)):
1. Download the processed bam files (shRNA-seq and eCLIP-seq) from [ENCODE](https://www.encodeproject.org) portal.
1. Download transcriptome quantification of [TCGA](https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga) and [GTEx](https://commonfund.nih.gov/gtex) projects from [Xena](https://xena.ucsc.edu).
1. Run `xena.R`, `encode_surf_one.R` (for each RBP), and `encode_surf_summary.R` in order.
To reproduce the simulation results:
1. Download the processed bam files (Homo sapiens) from ArrayExpress dataset [E-MTAB-3766](https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3766/files/processed/).
1. Run `other_simulation.sh` and `drseq_simulation.R` in order.
## Contact
Fan Chen (fan.chen@wisc.edu) or Sunduz Keles (keles@stat.wisc.edu)
## Reference
Chen F and Keles S. "SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins."