Package: LongOmicsTraj
Type: Package
Title: Longitudinal Omics Trajectory Clustering and Analysis Engine
Version: 0.99.0
Authors@R: 
    person(
        given = "Nazanin",
        family = "Zounemat-Kermani",
        email = "nonakermani@gmail.com",
        role = c("aut", "cre"),
        comment = c(
            ORCID = "0000-0003-2479-3861"
        )
    )
Description: Provides methods for estimating, classifying and comparing
        longitudinal molecular trajectories across repeated study
        visits using empirical, mixed-effects, generalized additive
        model and polynomial regression estimators. Consecutive
        molecular changes are converted into interpretable Omics
        Trajectory Signatures (OTS) describing stable, sustained,
        transient and rebound temporal behaviours, enabling topology-
        aware clustering and consensus trajectory inference.
        LongOmicsTraj further provides a flexible query framework for
        directly retrieving molecular features satisfying simple or
        complex trajectory definitions, including multi-transition
        patterns, logical combinations of trajectory states,
        group-specific behaviours, and comparisons of trajectory
        topologies across treatment arms, experimental conditions or
        other longitudinal study arms.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.5.0), MultiAssayExperiment
Imports: methods, data.table, S4Vectors, SummarizedExperiment,
        BiocParallel, ggplot2, dplyr, tibble, tidyr, rlang, scales,
        withr, stats4, lme4, emmeans, mgcv
Suggests: testthat (>= 3.0.0), matrixStats, cluster, knitr, rmarkdown,
        flexmix, patchwork, BiocStyle, maSigPro
VignetteBuilder: knitr
biocViews: Software, TimeCourse, Transcriptomics, Clustering,
        SystemsBiology
BugReports: https://github.com/nzkermani/LongOmicsTraj/issues
URL: https://github.com/nzkermani/LongOmicsTraj
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake make libicu-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-08-04 00:18:46 UTC
RemoteUrl: https://github.com/BiocStaging/LongOmicsTraj
RemoteRef: HEAD
RemoteSha: c92f35a6d48426c6164fd02a12b89bec01bddeec
NeedsCompilation: no
Packaged: 2026-10-03 10:41:03 UTC; root
Author: Nazanin Zounemat-Kermani [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2479-3861>)
Maintainer: Nazanin Zounemat-Kermani <nonakermani@gmail.com>