swissrepeat

Collaboration with ZHAW and Stockholm University on annotation and analysis of the SwissProt database in terms of tandem repeats and disorder.

Publication

Delucchi, M.; Schaper, E.; Sachenkova, O.; Elofsson, A.; Anisimova, M.
A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder.
Genes 2020, 11, 407. https://doi.org/10.3390/genes11040407

Getting Started

These instructions will get you a copy of the project up and running on your local machine to reproduce the published results.

Prerequisites

R version 3.6.2
R studio version >1.2.5

Installing

Clone this repository and cd in ./results/

Make a copy of local_config_TEMPLATE.R by:

cp local_config_TEMPLATE.R local_config.R

In the newly created local_config.R specify system specific configurations.

Install the required R-packages:

install.packages("plyr")
install.packages("pals") # nice color gradients
install.packages("ggplot2")
install.packages("scales")
install.packages("grid")
install.packages("RColorBrewer")
install.packages("tidyverse")
install.packages("ggrepel")
install.packages("xtable")
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("Biostrings")
install.packages("doParallel")
install.packages("foreach")
install.packages("taxize")
install.packages("UpSetR")
install.packages("reshape2")