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HPiP

Host-Pathogen Interaction Prediction


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HPiP")

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

Documentation

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

browseVignettes("HPiP")
Introduction to HPiP HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GenePrediction, Network, NetworkInference, Proteomics, Software, StructuralPrediction, SystemsBiology
Version 1.8.0
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
See More
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_1.8.0.tar.gz
Windows Binary HPiP_1.8.0.zip
macOS Binary (x86_64) HPiP_1.8.0.tgz
macOS Binary (arm64) HPiP_1.8.0.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/
Package Downloads Report Download Stats