HPiP

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

Host-Pathogen Interaction Prediction

Bioconductor version: Development (3.21)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GenePrediction, Network, NetworkInference, Proteomics, Software, StructuralPrediction, SystemsBiology
Version	1.13.0
In Bioconductor since	BioC 3.14 (R-4.1) (3 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

Suggests	rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	HPiP_1.13.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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