# Support code for Ncube-Kanyika et.al. (2022) CASSAVA PROTEINS INTERACTING WITH THE MOVEMENT PROTEIN OF SOUTH AFRICAN CASSAVA MOSAIC VIRUS REVEAL ROLES IN PATHOGENICITY.
By Valeria Velásquez-Zapata
Overview
This repository contains code for performing the bioinformatic analysis of the manuscript. It is separated in two R scripts with instruction on how to format the files to run the SAINTexpress and Y2H-SCORES software in analysis of MS Co-IP data and for posterior network analysis .
Citations
If you use part of this code please cite
- Ncube-Kanyika B, Velásquez-Zapata V, Wise RP, Rey MEC (2022). Cassava proteins interacting with the movement protein of south African cassava mosaic virus reveal roles in pathogenicity.
Software requirements
- R
- R packages: UniprotR, stringr, reshape2, tidyverse, psych, DESeq2, mass, igraph, RCy3
- Unix
Functions in this repository
Two R files were created with the main functions used to perform the analysis. A brief description of each file is provided:
-
SAINTexpress and Y2H-SCORES analyses.R
contains the formatting of files to run SAINTexpress and Y2H-SCORES. -
BC1_subnetwork_analysis.R
contains network analysis of the BC1 interactors in a compiled Arabidopsis interactome.