This is the
released
version of HPiP; for the devel version, see
HPiP
Host-Pathogen Interaction Prediction
Bioconductor version:
Release (3.22)
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
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
1.16.1
In Bioconductor since
BioC 3.14 (R-4.1) (4.5 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
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colorspace
e1071
kernlab
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SummarizedExperiment
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gridExtra
ggthemes
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RUnit
, tools,
knitr
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Installation
instructions to use this package in your R session.