HANDPrediction: toward sequence-based diagnosis of HIV-associated neurocognitive disorder (HAND)

Introduction

This is the R package for the prediction of the probability of HAND for given patients from sets of HIV envelope C2V3C3 sequences.

• Users should prepare following files; (1) env C2V3C3 alignment in FASTA format; (2) metadata; (3) sample source category design sheet.
• Users are recommended to prepare their alignment using HIVAlign tool with the HMM-align checkbox checked.
• The metadata should contain columns named as 'SequenceID', 'Clinical.Status' and 'Sample.Tissue'.
• The sample shource design sheet should contain columns named as 'Sample.Tissue' and 'Sample.Tissue.Category'. Currently, only supported Sample.Tissue.Category values are 'CNS', 'Blood', 'Lymph', and 'Others'.

Installation

1. Install the latest version of R (>=3.4.1) and RStudio.
2. Upgrade Bioconductor to the latest version (>=3.5).
3. Install the package HANDPrediction.

if(!require(devtools)) install.packages("devtools")
devtools::install_github("masato-ogishi/HANDPrediction")

# Alternatively, please download this repository as a Zip file, unzip it to the directory you want, and run the following command.
devtools::install_local("path/to/the/unzipped/folder")

Reference

• Masato Ogishi and Hiroshi Yotsuyanagi. Prediction of HIV-associated neurocognitive disorder (HAND) from three genetic features of envelope gp120 glycoprotein. Retrovirology. 2018 Jan 27;15(1):12. doi: 10.1186/s12977-018-0401-x.