Package: scMaSigPro
Type: Package
Title: Differential Expression Analysis Along Single-Cell Trajectories
Version: 0.6.0
Authors@R: c(
    person("Ana", "Conesa", role = "aut", email = "ana.conesa@csic.es",
           comment = c(ORCID = "0000-0001-9597-311X")),
    person("María José", "Nueda", role = "aut", email = "mj.nueda@ua.es",
           comment = c(ORCID = "0000-0002-1666-4771")),
    person("Priyansh", "Srivastava", role = c("aut", "cre"),
           email = "spriyansh29@gmail.com",
           comment = c(ORCID = "0000-0003-2618-5296")),
    person("Marta", "Benegas Coll", role = "aut", email = "martabc22@gmail.com",
           comment = c(ORCID = "0009-0004-9886-2828")),
    person("European Union", role = "fnd",
           comment = "Horizon 2020 Marie Skłodowska-Curie Grant Agreement No 953407"))
Description: Identifies genes whose expression changes along
        single-cell pseudotime and differs between the branching paths
        of a trajectory. Cells are pseudo-bulked into pseudotime bins
        that preserve their ordering, and the polynomial generalised
        linear model of the 'maSigPro' package is fitted to the binned
        counts with a negative binomial family and size-factor offsets.
        Methods are described in Srivastava et al. (2024)
        <doi:10.1093/bioinformatics/btae443>.
License: GPL (>= 2)
Imports: methods, stats, Matrix, S4Vectors (>= 0.40.2),
        SummarizedExperiment, SingleCellExperiment (>= 1.24.0), MASS,
        ggplot2, BiocParallel
Depends: R (>= 4.6.0)
Encoding: UTF-8
Language: en-GB
Roxygen: list(markdown = TRUE)
Suggests: testthat, roxygen2, knitr, rmarkdown, BiocStyle, UpSetR,
        patchwork, mclust, rlang, pkgload, maSigPro (>= 1.74.0),
        igraph, slingshot, DelayedMatrixStats
Config/testthat/edition: 3
URL: https://github.com/BioBam/scMaSigPro/,
        https://spriyansh.github.io/scMaSigPro/
biocViews: Clustering, Regression, TimeCourse, DifferentialExpression,
        GeneExpression, RNASeq, Sequencing, Software, SingleCell,
        Transcriptomics, MultipleComparison, Visualization
BugReports: https://github.com/BioBam/scMaSigPro/issues
VignetteBuilder: knitr
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: zlib1g-dev
Repository: https://spriyansh.r-universe.dev
Date/Publication: 2026-10-28 06:55:07 UTC
RemoteUrl: https://github.com/spriyansh/scMaSigPro
RemoteRef: HEAD
RemoteSha: f7b543ea6091ac73db96185a10dc625866b1c08d
NeedsCompilation: no
Packaged: 2026-10-28 07:18:26 UTC; root
Author: Ana Conesa [aut] (ORCID: <https://orcid.org/0000-0001-9597-311X>),
  María José Nueda [aut] (ORCID: <https://orcid.org/0000-0002-1666-4771>),
  Priyansh Srivastava [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2618-5296>),
  Marta Benegas Coll [aut] (ORCID:
    <https://orcid.org/0009-0004-9886-2828>),
  European Union [fnd] (Horizon 2020 Marie Skłodowska-Curie Grant
    Agreement No 953407)
Maintainer: Priyansh Srivastava <spriyansh29@gmail.com>