title	author	date	output	navbar
Home	Kate Lawrenson, Marcos A. S. Fonseca, Felipe Segato, et. al.	November, 2019	html_document smart	left text href Home index.html text href Normalization and DEG analysis transc_paper_markdown.html text href One-class analysis prj.mkd.transcriptome.OC.html text href Superenhancer analysis se-analysis.html text href Cistrome analysis tf-analysis.html

knitr::opts_chunk$set(echo = TRUE)

Introduction

This document contains workflows, explaining how to perform all analysis described in A Study of High-Grade Serous Ovarian Cancer Origins Implicates the SOX18 Transcription Factor in Tumor Development.

https://lawrenson-lab.github.io/OvarianRNASeq/index.html

Document authors

Marcos A. S. Fonseca & Felipe Segato.

Install packages

To install the required packages to run the code below please execute the follwing code.

deps <- c("gelnet","dplyr","gdata","DT", "TxDb.Hsapiens.UCSC.hg19.knownGene", "org.Hs.eg.db", "GenomicRanges")
for(pkg in deps)  if (!pkg %in% installed.packages()) install.packages(pkg, dependencies = TRUE)

Available files

• Superenhacers BED peaks.
• Pre-processed RData.
• Raw feature counts text file
• Cistrome BED peaks