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This is the development version of HPiP; for the stable release version, see HPiP.

Host-Pathogen Interaction Prediction

Bioconductor version: Development (3.19)

HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins.The proposed package can effectively address data shortages and data unavailability for HP-PPI network reconstructions. Moreover, establishing computational frameworks in that regard will reveal mechanistic insights into infectious diseases and suggest potential HP-PPI targets, thus narrowing down the range of possible candidates for subsequent wet-lab experimental validations.

Author: Matineh Rahmatbakhsh [aut, trl, cre], Mohan Babu [led]

Maintainer: Matineh Rahmatbakhsh <matinerb.94 at gmail.com>

Citation (from within R, enter citation("HPiP")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to HPiP HTML R Script
Reference Manual PDF


biocViews GenePrediction, Network, NetworkInference, Proteomics, Software, StructuralPrediction, SystemsBiology
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports dplyr (>= 1.0.6), httr (>= 1.4.2), readr, tidyr, tibble, utils, stringr, magrittr, caret, corrplot, ggplot2, pROC, PRROC, igraph, graphics, stats, purrr, grDevices, protr, MCL
System Requirements
URL https://github.com/mrbakhsh/HPiP
Bug Reports https://github.com/mrbakhsh/HPiP/issues
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Suggests rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HPiP_1.9.0.tar.gz
Windows Binary HPiP_1.9.0.zip (64-bit only)
macOS Binary (x86_64) HPiP_1.9.0.tgz
macOS Binary (arm64) HPiP_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/HPiP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HPiP
Bioc Package Browser https://code.bioconductor.org/browse/HPiP/
Package Short Url https://bioconductor.org/packages/HPiP/
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