recipe bioconductor-lpeadj

A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.

Homepage:

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

License:

LGPL

Recipe:

/bioconductor-lpeadj/meta.yaml

Links:

biotools: lpeadj, doi: 10.1038/nmeth.3252

Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment.

package bioconductor-lpeadj

(downloads) docker_bioconductor-lpeadj

Versions:
1.62.0-0,  1.60.0-0,  1.58.0-0,  1.54.0-0,  1.52.0-0,  1.50.0-1,  1.50.0-0,  1.48.0-0,  1.46.0-0, 

1.62.0-0,  1.60.0-0,  1.58.0-0,  1.54.0-0,  1.52.0-0,  1.50.0-1,  1.50.0-0,  1.48.0-0,  1.46.0-0,  1.44.0-1,  1.44.0-0,  1.42.0-0,  1.40.0-0,  1.38.0-0

Depends:

  • on bioconductor-lpe >=1.76.0,<1.77.0

  • on r-base >=4.3,<4.4.0a0

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-lpeadj

to add into an existing workspace instead, run:

pixi add bioconductor-lpeadj

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-lpeadj

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-lpeadj

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-lpeadj:<tag>

(see bioconductor-lpeadj/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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