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Bioconductor - HPiP

HPiP

This is the released version of HPiP; for the devel version, see HPiP.

Host-Pathogen Interaction Prediction

Bioconductor version: Release (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")

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")

Details biocViews GenePrediction, Network, NetworkInference, Proteomics, Software, StructuralPrediction, SystemsBiology Version 1.14.0 In Bioconductor since BioC 3.14 (R-4.1) (3.5 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.

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