MICSQTL

This is the development version of MICSQTL; for the stable release version, see MICSQTL.

MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)

Bioconductor version: Development (3.21)

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] (ORCID: ), Qian Li [aut, cre] (ORCID: ), Iain Carmichael [ctb]

Maintainer: Qian Li <qian.li at stjude.org>

Citation (from within R, enter citation("MICSQTL")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBasedAssays, Coverage, GeneExpression, Genetics, Proteomics, RNASeq, Sequencing, SingleCell, Software, Visualization
Version	1.5.0
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

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_1.5.0.tar.gz
Windows Binary (x86_64)	MICSQTL_1.5.0.zip
macOS Binary (x86_64)	MICSQTL_1.5.0.tgz
macOS Binary (arm64)	MICSQTL_1.5.0.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