hoxd13 Readme

About

Unblending of Transcriptional Condensates in Human Repeat Expansion Disease.

Published:May 07, 2020 DOI:https://doi.org/10.1016/j.cell.2020.04.018

Authors: Sebastian Mackowiak, Shaon Basu, Henri Niskanen, Dora Knezevic

This github contains mainly the computational analysis to the study.

Complementary data for running most of the R scripts can be found at Mendeley, doi: 10.17632/ztd6wzcv7h.13

Getting a copy

1a. You can checkout this repository by typing on the command line

git clone https://github.com/hniszlab/hoxd13.git

or

1b. download the zip file and extract it by typing

wget https://github.com/hniszlab/hoxd13/archive/master.zip -O hoxd13.zip
unzip hoxd13.zip

2. Change the directory of the hoxd13 project

cd hoxd13

Running the code

All R code and packages were run in R version 3.6.0 (2019-04-26)

Start an R console and install the necessary dependencies if they should be missing

R
library(dendextend)
library(cowplot)
library(svglite)
library(gplots)
library(Matrix)
library(Rtsne)
library(irlba)
library(raster)
library(RColorBrewer)
library(scales)
library(data.table)
library(argparse)
library(directlabels)

Missing R libraries can be installed by the install.packages command. E.g.

install.packages("Matrix")