Package: MICSQTL
Type: Package
Title: MICSQTL (Multi-omic deconvolution, Integration and
        Cell-type-specific Quantitative Trait Loci)
Version: 1.6.0
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
git_url: https://git.bioconductor.org/packages/MICSQTL
git_branch: RELEASE_3_21
git_last_commit: 8d88ac3
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 01:58:12 UTC; biocbuild
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 4.5.0; ; 2025-04-16 14:53:39 UTC; windows
