2019-nCoV-T-Cell-Vaccine-Candidates

Prerequisites

Latest version of R (version 3.6.0 or later) and RStudio (version 1.2.5 or later) installed.

Set the working directory to the downloaded repository folder in local system.

Following R packages and their dependencies are required.

+ here 
+ RColorBrewer 
+ tidyverse 
+ seqinr
+ readxl 
+ readr 
+ glue 
+ reticulate 
+ BALCONY 
+ seqinr 
+ doParallel
+ BiocManager
+ msa 
+ Biostrings
+ doParallel
+ foreach

Organization

• Main R code is in main.R file.
• Scripts for preparation of raw genomic sequences is in preparation.R
• Custom functions are in Functions folder
• All data files are in Data folder
• Python 2.7 code from IEDB for computing population coverages is in Utils folder
• MAFFT v7 source code for Linux operating system downloaded from here

Main Project File

• Open the main.R R script file in RStudio and run. This will run the analysis reproduce the results.
• Outputs will be in Data folder.
• Preparation.R will work only with Linux MAFFT software installed and available on the system.
• Population coverage code works only with an available Conda Python 2.7 environment (named as "py27") on the system.
• If the said Conda environment is not avaialable then the population coverages can be computed online using IEDB Analysis Resource.
  • Select the "Population" (China or World).
  • Select "Calculation option" (Class I and II combined)
  • Proide one of the following files (located within Data folder) to the option "Enter epitope / MHC restriction data in the form below or select a file":
    • Tcell_epitopes_China (for computing coverages for set of MHC alleles identified to maximize population coverage in China.)
    • Tcell_epitopes_World (for computing coverages for set of MHC alleles identified to maximize global population coverage.)

Troubleshooting

For any questions or comments related to the code and data, please send email to: [email protected].