Package Recipe 'bioconductor-micsqtl'

recipe bioconductor-micsqtl

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

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/MICSQTL.html
License:: GPL-3
Recipe:: /bioconductor-micsqtl/meta.yaml

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.

package bioconductor-micsqtl¶

Versions:

1.8.0-0, 1.4.0-0

Depends:

on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-toast >=1.24.0,<1.25.0
on r-base >=4.5,<4.6.0a0
on r-dirmult
on r-ggplot2
on r-ggpubr
on r-ggridges
on r-glue
on r-magrittr
on r-nnls
on r-purrr
on r-tca

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-micsqtl

to add into an existing workspace instead, run:

pixi add bioconductor-micsqtl

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-micsqtl

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-micsqtl

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-micsqtl:<tag>

(see bioconductor-micsqtl/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-micsqtl/README.html)