recipe bioconductor-differentialregulation

Differentially regulated genes from scRNA-seq data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/DifferentialRegulation.html

License:

GPL-3

Recipe:

/bioconductor-differentialregulation/meta.yaml

DifferentialRegulation is a method for detecting differentially regulated genes between two groups of samples (e.g., healthy vs. disease, or treated vs. untreated samples), by targeting differences in the balance of spliced and unspliced mRNA abundances, obtained from single-cell RNA-sequencing (scRNA-seq) data. From a mathematical point of view, DifferentialRegulation accounts for the sample-to-sample variability, and embeds multiple samples in a Bayesian hierarchical model. Furthermore, our method also deals with two major sources of mapping uncertainty: i) 'ambiguous' reads, compatible with both spliced and unspliced versions of a gene, and ii) reads mapping to multiple genes. In particular, ambiguous reads are treated separately from spliced and unsplced reads, while reads that are compatible with multiple genes are allocated to the gene of origin. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques (Metropolis-within-Gibbs).

package bioconductor-differentialregulation

versions:

2.0.2-0,  1.4.2-0,  1.2.0-1,  1.2.0-0

depends bioconductor-bandits:

>=1.18.0,<1.19.0

depends bioconductor-bandits:

>=1.18.1,<1.19.0a0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0a0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0a0

depends bioconductor-tximport:

>=1.30.0,<1.31.0

depends bioconductor-tximport:

>=1.30.0,<1.31.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-doparallel:

depends r-dorng:

depends r-foreach:

depends r-ggplot2:

depends r-gridextra:

depends r-mass:

depends r-matrix:

depends r-rcpp:

depends r-rcpparmadillo:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-differentialregulation

and update with::

   mamba update bioconductor-differentialregulation

To create a new environment, run:

mamba create --name myenvname bioconductor-differentialregulation

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `bioconductor-differentialregulation/tags`_ for valid values for ``<tag>``)

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