/swissrepeats

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.

Primary LanguageHTMLMIT LicenseMIT

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")