README.md

In elmerfer/RAPInetMHCpan: an R API to netMHCpan and netMHCIIpan softwares for neural network prediction of peptide binders

RAPInetMHCpan

RAPInetMHCpan: a library to facilitate the installation and use of both netMHCpan and netMHCIIpan neural networks for prediction of peptides binding to MHC molecules (up to now only available for Linux, Mac in progress)

Installation of the library RAPInetMHCpan

You may choose one of the following choices (please check the prerequisites)

Download the precomplied version and install from R console or RStudio

download the precompiled version of RAPInetMHCpan, then use

install.packages("...../RAPInetMHCpan_0.1.0.tar.gz", repos = NULL, type = "source")

Install from GitHub

First, you need to install the devtools package. You can do this from CRAN. Invoke R and then type

install.packages("devtools")

Load the devtools package.

library(devtools)
install_github("elmerfer/RAPInetMHCpan")

Prerequisites

You will need to install from CRAN openxlsx ggplot2 stringr seqinr * ggseqlogo

You will need to install from Bioconductor * BiocParallel

Before the installation of netMHCpan and netMHCIIpan

Please be sure that you have the right shell to run netMHCpan and netMHCIIpan. They both use the "tcsh", a Unix based shell compatible with cshel (a shel to run c code).

Installing the netMHCpan and netMHCIIpan softwares

Check if the appropriate C shell is installed in your machine

To verify if you have it in your machine, please type from a console terminal the following command 'tsch --version' if succeed you will see something like this: if not installed try 'sudo apt-get install tcsh' and verify.

If it is done, you may continue installing netMHCpan and netMHCIIpan through RAPInetMHCpan

Installation of netMHCpan and netMHCIIpan with RAPInetMHCpan into R

Follow the instructions and fill the form to receive the rights to download netMHCpan and netMHCIIpan and save them to your favorite directory. Onpen an R session or RStudio and type:

library(RAPInetMHCpan)
installNetMHCPan(file = "/home/.../myfavoritedir/netMHCpan-VERSION.Linux.tar.gz" , data = NULL, dir = "/where i whant/dir")
installNetMHCIIPan(file = "/home/.../myfavoritedir/netMHCIIpan-VERSION.Linux.tar.gz" , data = NULL, dir = "/where i whant/dir")

It will print on console:

netMHCpan Installation OK

or

netMHCIIpan Installation OK

Testing the library

Please download and run the following R script file test.rapiNetMHCpan

Authors

• Elmer A. Fernández - Idea and Initial work - Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas (CIDIE) - Univ. Católica de Córdoba - CONICET, Argentina
• Macarena Rodriguez Walker - Sequence analysis - Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas (CIDIE) - Univ. Católica de Córdoba - CONICET, Argentina

License

This project is licensed under the GPL 3-0 License

Sotware citation

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data. Vanessa Jurtz 1, Sinu Paul 2, Massimo Andreatta, Paolo Marcatili, Bjoern Peters, and Morten Nielsen. The Journal of Immunology (2017) ji1700893; DOI: 10.4049/jimmunol.1700893

Improved prediction of MHC II antigen presentation through integration and motif deconvolution of mass spectrometry MHC eluted ligand data. Reynisson B, Barra C, Kaabinejadian S, Hildebrand WH, Peters B, Nielsen M. J Proteome Res 2020 Apr 30. doi: 10.1021/acs.jproteome.9b00874.

elmerfer/RAPInetMHCpan documentation built on Sept. 17, 2021, 2:14 p.m.