Package Recipe 'bioconductor-scan.upc'

recipe bioconductor-scan.upc

Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/SCAN.UPC.html
License:: MIT
Recipe:: /bioconductor-scan.upc/meta.yaml
Links:: biotools: scan.upc

SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration.

package bioconductor-scan.upc¶

Versions:

2.52.0-0, 2.48.0-0, 2.44.0-0, 2.42.0-0, 2.40.0-0, 2.36.0-0, 2.34.0-0, 2.32.0-1, 2.32.0-0,

2.52.0-0, 2.48.0-0, 2.44.0-0, 2.42.0-0, 2.40.0-0, 2.36.0-0, 2.34.0-0, 2.32.0-1, 2.32.0-0, 2.30.0-0, 2.28.0-0, 2.26.0-1, 2.24.1-0, 2.22.0-0, 2.20.0-0, 2.18.0-0

Depends:

on bioconductor-affy >=1.88.0,<1.89.0
on bioconductor-affyio >=1.80.0,<1.81.0
on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-geoquery >=2.78.0,<2.79.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-oligo >=1.74.0,<1.75.0
on bioconductor-sva >=3.58.0,<3.59.0
on r-base >=4.5,<4.6.0a0
on r-foreach
on r-mass

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-scan.upc

to add into an existing workspace instead, run:

pixi add bioconductor-scan.upc

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-scan.upc

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-scan.upc

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-scan.upc:<tag>

(see bioconductor-scan.upc/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-scan.upc/README.html)