Package: MICSQTL
Type: Package
Title: MICSQTL (Multi-omic deconvolution, Integration and
        Cell-type-specific Quantitative Trait Loci)
Version: 1.8.0
Authors@R: c(person("Yue", "Pan", role = "aut",
                     email = "ypan@stjude.org",
                     comment = c(ORCID = "0000-0003-1958-2744")),
             person("Qian", "Li", role = c("aut","cre"),
                     email = "qian.li@stjude.org",
                     comment=c(ORCID="0000-0001-9874-3555")),
             person("Iain", "Carmichael", role = "ctb",
                     email = "iain@berkeley.edu"))
Description: Our pipeline, MICSQTL, utilizes scRNA-seq reference and
        bulk transcriptomes to estimate cellular composition in the
        matched bulk proteomes. The expression of genes and proteins at
        either bulk level or cell type level can be integrated by
        Angle-based Joint and Individual Variation Explained (AJIVE)
        framework. Meanwhile, MICSQTL can perform cell-type-specic
        quantitative trait loci (QTL) mapping to proteins or
        transcripts based on the input of bulk expression data and the
        estimated cellular composition per molecule type, without the
        need for single cell sequencing. We use matched
        transcriptome-proteome from human brain frontal cortex tissue
        samples to demonstrate the input and output of our tool.
License: GPL-3
Encoding: UTF-8
Suggests: testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle
VignetteBuilder: knitr
biocViews: GeneExpression, Genetics, Proteomics, RNASeq, Sequencing,
        SingleCell, Software, Visualization, CellBasedAssays, Coverage
Imports: TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2,
        ggpubr, ggridges, glue, S4Vectors, dirmult
Depends: R (>= 4.3.0), SummarizedExperiment, stats
RoxygenNote: 7.2.3
LazyData: false
Config/testthat/edition: 3
URL: https://bioconductor.org/packages/MICSQTL,
        https://github.com/YuePan027/MICSQTL
BugReports: https://github.com/YuePan027/MICSQTL/issues
Config/pak/sysreqs: cmake make libicu-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:24:12 UTC
RemoteUrl: https://github.com/bioc/MICSQTL
RemoteRef: RELEASE_3_22
RemoteSha: d51e216fdb2cde1e93d03970deb1c05c85873c7e
NeedsCompilation: no
Packaged: 2026-02-25 09:33:34 UTC; root
Author: Yue Pan [aut] (ORCID: <https://orcid.org/0000-0003-1958-2744>),
  Qian Li [aut, cre] (ORCID: <https://orcid.org/0000-0001-9874-3555>),
  Iain Carmichael [ctb]
Maintainer: Qian Li <qian.li@stjude.org>
Built: R 4.5.2; ; 2026-02-25 09:35:34 UTC; windows
