Package Recipe 'bioconductor-cagefightr'

recipe bioconductor-cagefightr

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/CAGEfightR.html
License:: GPL-3 + file LICENSE
Recipe:: /bioconductor-cagefightr/meta.yaml

CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.

package bioconductor-cagefightr¶

Versions:

1.30.0-0, 1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.10.0-0,

1.30.0-0, 1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.10.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-1, 1.2.0-1, 1.2.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-genomicalignments >=1.46.0,<1.47.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicfiles >=1.46.0,<1.47.0
on bioconductor-genomicinteractions >=1.44.0,<1.45.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-gviz >=1.54.0,<1.55.0
on bioconductor-interactionset >=1.38.0,<1.39.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-assertthat >=0.2.0
on r-base >=4.5,<4.6.0a0
on r-matrix >=1.2-12
on r-pryr >=0.1.3

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-cagefightr

to add into an existing workspace instead, run:

pixi add bioconductor-cagefightr

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-cagefightr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cagefightr

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-cagefightr:<tag>

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