Package Recipe 'r-tailfindr'

recipe r-tailfindr

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.

Homepage:: https://github.com/adnaniazi/tailfindr
License:: AGPL-3.0
Recipe:: /r-tailfindr/meta.yaml

package r-tailfindr¶

Versions:

1.4-3, 1.4-2, 1.4-1, 1.4-0, 1.3-2, 1.3-1, 1.3-0, 1.2-3, 1.2-2,

1.4-3, 1.4-2, 1.4-1, 1.4-0, 1.3-2, 1.3-1, 1.3-0, 1.2-3, 1.2-2, 1.2-1, 1.2-0

Depends:

on bioconductor-biostrings >=2.74.0,<2.75.0a0
on bioconductor-rsamtools
on libgcc >=13
on libstdcxx >=13
on r-base >=4.4,<4.5.0a0
on r-cli
on r-crayon
on r-data.table
on r-doparallel
on r-dosnow
on r-dplyr
on r-ggplot2
on r-hdf5r
on r-knitr
on r-magrittr
on r-plyr
on r-psych
on r-purrr
on r-r.utils
on r-rbokeh
on r-rcpp
on r-rcurl
on r-rmarkdown
on r-stringr
on r-testthat
on r-tibble
on r-tidyr
on r-xml

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-tailfindr

to add into an existing workspace instead, run:

pixi add r-tailfindr

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-tailfindr

Alternatively, to install into a new environment, run:

conda create -n envname r-tailfindr

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-tailfindr:<tag>

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