recipe bioconductor-oscope

Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/Oscope.html

License:

Artistic-2.0

Recipe:

/bioconductor-oscope/meta.yaml

Links:

biotools: oscope, doi: 10.1038/nmeth.3549

Oscope is a statistical pipeline developed to identifying and recovering the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. The Oscope pipeline includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.

package bioconductor-oscope

(downloads) docker_bioconductor-oscope

Versions:
1.40.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0, 

1.40.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.1-0,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-0

Depends:

  • on bioconductor-biocparallel >=1.44.0,<1.45.0

  • on bioconductor-ebseq >=2.8.0,<2.9.0

  • on r-base >=4.5,<4.6.0a0

  • on r-cluster

  • on r-testthat

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-oscope

to add into an existing workspace instead, run:

pixi add bioconductor-oscope

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-oscope

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-oscope

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-oscope:<tag>

(see bioconductor-oscope/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.

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