Package Recipe 'r-tsenat'

recipe r-tsenat

Tsallis Entropy Analysis Toolbox for transcriptome complexity analysis

Homepage:: https://github.com/gallardoalba/TSENAT
Documentation:: https://gallardoalba.github.io/TSENAT
License:: GPL-3.0-or-later
Recipe:: /r-tsenat/meta.yaml

Quantifies and models isoform-usage complexity in RNA-seq data using Tsallis entropy, a scale-dependent diversity measure. TSENAT computes q-dependent transcriptome diversity and divergence, compares measures between conditions, and provides visualization routines for scale-dependent complexity analysis.

package r-tsenat¶

Versions:

0.99.0-1, 0.99.0-0

Depends:

on __glibc >=2.17,<3.0.a0
on bioconductor-biocparallel >=1.44.0,<1.45.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0
on libgcc >=14
on libstdcxx >=14
on r-base >=4.5,<4.6.0a0
on r-cowplot
on r-digest
on r-dplyr
on r-fdrtool
on r-gamsel
on r-geepack
on r-ggplot2
on r-glmmtmb
on r-glmnet
on r-gridextra
on r-matrixstats
on r-memoise
on r-mgcv
on r-nlme
on r-patchwork
on r-pheatmap
on r-rcolorbrewer
on r-rcpp
on r-rcpparmadillo
on r-readr
on r-rlang
on r-tidyr
on r-withr

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 r-tsenat

to add into an existing workspace instead, run:

pixi add r-tsenat

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 r-tsenat

Alternatively, to install into a new environment, run:

conda create -n envname r-tsenat

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/r-tsenat:<tag>

(see r-tsenat/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/r-tsenat/README.html)