MICSQTL

DOI: 10.18129/B9.bioc.MICSQTL  

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

Bioconductor version: Release (3.18)

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, cre] , Qian Li [aut], Iain Carmichael [ctb]

Maintainer: Yue Pan <ypan at stjude.org>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	MICSQTL: Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, Coverage, GeneExpression, Genetics, Proteomics, RNASeq, Sequencing, SingleCell, Software, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	GPL-3
Depends	R (>= 4.3.0), SummarizedExperiment, stats
Imports	TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2, ggpubr, ggridges, glue, S4Vectors, dirmult
LinkingTo
Suggests	testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MICSQTL_1.0.0.tar.gz
Windows Binary	MICSQTL_1.0.0.zip
macOS Binary (x86_64)	MICSQTL_1.0.0.tgz
macOS Binary (arm64)	MICSQTL_1.0.0.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
Old Source Packages for BioC 3.18	Source Archive