Package Recipe 'bioconductor-blima'

recipe bioconductor-blima

Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/blima.html
License:: GPL-3
Recipe:: /bioconductor-blima/meta.yaml
Links:: biotools: blima, doi: 10.1038/nmeth.3252

Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.

package bioconductor-blima¶

Versions:

1.40.0-0, 1.36.0-0, 1.34.0-0, 1.32.0-1, 1.32.0-0, 1.28.0-2, 1.28.0-1, 1.28.0-0, 1.26.0-0,

1.40.0-0, 1.36.0-0, 1.34.0-0, 1.32.0-1, 1.32.0-0, 1.28.0-2, 1.28.0-1, 1.28.0-0, 1.26.0-0, 1.24.0-1, 1.24.0-0, 1.22.0-0, 1.20.0-0, 1.18.0-1, 1.16.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-0

Depends:

on bioconductor-beadarray >=2.56.0,<2.57.0
on bioconductor-beadarray >=2.56.0,<2.57.0a0
on bioconductor-biobase >=2.66.0,<2.67.0
on bioconductor-biobase >=2.66.0,<2.67.0a0
on bioconductor-biocgenerics >=0.52.0,<0.53.0
on bioconductor-biocgenerics >=0.52.0,<0.53.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=13
on liblapack >=3.9.0,<4.0a0
on libstdcxx >=13
on r-base >=4.4,<4.5.0a0
on r-rcpp >=0.12.8

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-blima

to add into an existing workspace instead, run:

pixi add bioconductor-blima

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-blima

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-blima

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-blima:<tag>

(see bioconductor-blima/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-blima/README.html)