Package: netOmics

Title: Multi-Omics (time-course) network-based integration and interpretation

Version: 1.11.1

Authors@R: 

    person(given = "Antoine", family = "Bodein", role = c("aut", "cre"), email = "antoine.bodein.1@ulaval.ca")

Description: netOmics is a multi-omics networks builder and explorer.

    It uses a combination of network inference algorithms and and knowledge-based graphs to build multi-layered networks.

    The package can be combined with timeOmics to incorporate time-course expression data and build sub-networks from multi-omics kinetic clusters.

    Finally, from the generated multi-omics networks, propagation analyses allow the identification of missing biological functions (1), 

    multi-omics mechanisms (2) and molecules between kinetic clusters (3). This helps to resolve complex regulatory mechanisms.

License: GPL-3

Encoding: UTF-8

LazyData: false

Roxygen: list(markdown = TRUE)

RoxygenNote: 7.3.1

VignetteBuilder: knitr

Depends: R (>= 4.1)

Imports: 

    dplyr, 

    ggplot2, 

    igraph, 

    magrittr, 

    minet, 

    purrr, 

    tibble, 

    tidyr, 

    AnnotationDbi, 

    GO.db, 

    gprofiler2,

    methods,

    Matrix,

    stats

Suggests: 

    mixOmics,

    timeOmics,

    tidyverse,

    BiocStyle,

    testthat,

    covr,

    rmarkdown,

    knitr

biocViews: GraphAndNetwork, Software, TimeCourse, WorkflowStep, SystemsBiology, NetworkInference, Network

URL: https://github.com/abodein/netOmics

BugReports: https://github.com/abodein/netOmics/issues

PackageStatus: Deprecated