HPiP

DOI: 10.18129/B9.bioc.HPiP    

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

Host-Pathogen Interaction Prediction

Bioconductor version: Development (3.15)

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 "4.2") and enter:

if (!requireNamespace("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")

 

HTML R Script Introduction to HPiP
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews GenePrediction, Network, NetworkInference, Proteomics, Software, StructuralPrediction, SystemsBiology
Version 1.1.1
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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
LinkingTo
Suggests rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr
SystemRequirements
Enhances
URL https://github.com/mrbakhsh/HPiP
BugReports https://github.com/mrbakhsh/HPiP/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package HPiP_1.1.1.tar.gz
Windows Binary
macOS 10.13 (High Sierra) HPiP_1.1.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/HPiP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HPiP
Package Short Url https://bioconductor.org/packages/HPiP/
Package Downloads Report Download Stats

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