Package Recipe 'bioconductor-linnorm'

recipe bioconductor-linnorm

Linear model and normality based normalization and transformation method (Linnorm)

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/Linnorm.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-linnorm/meta.yaml
Links:: biotools: linnorm

Linnorm is an algorithm for normalizing and transforming RNA-seq, single cell RNA-seq, ChIP-seq count data or any large scale count data. It has been independently reviewed by Tian et al. on Nature Methods (https://doi.org/10.1038/s41592-019-0425-8). Linnorm can work with raw count, CPM, RPKM, FPKM and TPM.

package bioconductor-linnorm¶

Versions:

2.34.0-0, 2.30.0-0, 2.26.0-1, 2.26.0-0, 2.24.1-0, 2.22.0-1, 2.22.0-0, 2.18.0-2, 2.18.0-1,

2.34.0-0, 2.30.0-0, 2.26.0-1, 2.26.0-0, 2.24.1-0, 2.22.0-1, 2.22.0-0, 2.18.0-2, 2.18.0-1, 2.18.0-0, 2.16.0-0, 2.14.0-1, 2.14.0-0, 2.12.0-0, 2.10.0-0, 2.8.0-1, 2.8.0-0, 2.6.1-0, 2.6.0-0

Depends:

on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-limma >=3.66.0,<3.67.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-amap
on r-apcluster
on r-base >=4.5,<4.6.0a0
on r-ellipse
on r-fastcluster
on r-fpc
on r-ggdendro
on r-ggplot2
on r-gmodels
on r-igraph
on r-mass
on r-mclust
on r-rcpp >=0.12.2
on r-rcpparmadillo >=0.8.100.1.0
on r-rtsne
on r-statmod
on r-vegan
on r-zoo

Additional platforms:

linux-aarch64

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-linnorm

to add into an existing workspace instead, run:

pixi add bioconductor-linnorm

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-linnorm

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-linnorm

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-linnorm:<tag>

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