DOI: 10.18129/B9.bioc.HPiP  

Host-Pathogen Interaction Prediction

Bioconductor version: Release (3.17)

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>

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biocViews GenePrediction, Network, NetworkInference, Proteomics, Software, StructuralPrediction, SystemsBiology
Version 1.6.0
In Bioconductor since BioC 3.14 (R-4.1) (2 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
Suggests rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr
URL https://github.com/mrbakhsh/HPiP
BugReports https://github.com/mrbakhsh/HPiP/issues
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Source Package HPiP_1.6.0.tar.gz
Windows Binary HPiP_1.6.0.zip
macOS Binary (x86_64) HPiP_1.6.0.tgz
macOS Binary (arm64) HPiP_1.6.0.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/
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