MICSQTL
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see MICSQTL.
MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)
Bioconductor version: 3.19
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.
Author: Yue Pan [aut] 
, Qian Li [aut, cre] , Iain Carmichael [ctb]
Maintainer: Qian Li <qian.li at stjude.org>
citation("MICSQTL")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MICSQTL")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MICSQTL")| MICSQTL: Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, Coverage, GeneExpression, Genetics, Proteomics, RNASeq, Sequencing, SingleCell, Software, Visualization |
| Version | 1.2.2 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| License | GPL-3 |
| Depends | R (>= 4.3.0), SummarizedExperiment, stats |
| Imports | TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2, ggpubr, ggridges, glue, S4Vectors, dirmult |
| System Requirements | |
| URL | https://bioconductor.org/packages/MICSQTL https://github.com/YuePan027/MICSQTL |
| Bug Reports | https://github.com/YuePan027/MICSQTL/issues |
See More
| Suggests | testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MICSQTL_1.2.2.tar.gz |
| Windows Binary (x86_64) | MICSQTL_1.2.2.zip |
| macOS Binary (x86_64) | MICSQTL_1.2.2.tgz |
| macOS Binary (arm64) | MICSQTL_1.2.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MICSQTL |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MICSQTL |
| Bioc Package Browser | https://code.bioconductor.org/browse/MICSQTL/ |
| Package Short Url | https://bioconductor.org/packages/MICSQTL/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |