HPiP
This is the released version of HPiP; for the devel version, see HPiP.
Host-Pathogen Interaction Prediction
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.18.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (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_1.18.0.tar.gz |
| Windows Binary (x86_64) | HPiP_1.18.0.zip |
| macOS Binary (big-sur-x86_64) | HPiP_1.18.0.tgz |
| macOS Binary (sonoma-arm64) | HPiP_1.18.0.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/ |
| Package Downloads Report | Download Stats |