HPiP
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see HPiP.
Host-Pathogen Interaction Prediction
Bioconductor version: 3.16
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("HPiP")):
Installation
To install this package, start R (version "4.2") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GenePrediction, Network, NetworkInference, Proteomics, Software, StructuralPrediction, SystemsBiology |
| Version | 1.4.3 |
| 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 |
| 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_1.4.3.tar.gz |
| Windows Binary | HPiP_1.4.3.zip |
| macOS Binary (x86_64) | HPiP_1.4.3.tgz |
| macOS Binary (arm64) | HPiP_1.4.3.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 |
| Old Source Packages for BioC 3.16 | Source Archive |