recipe bioconductor-cagefightr

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

Homepage:

https://bioconductor.org/packages/3.17/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:

1.20.0-0,  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, 

1.20.0-0,  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 bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicalignments:

>=1.36.0,<1.37.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicfiles:

>=1.36.0,<1.37.0

depends bioconductor-genomicinteractions:

>=1.34.0,<1.35.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-gviz:

>=1.44.0,<1.45.0

depends bioconductor-interactionset:

>=1.28.0,<1.29.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends r-assertthat:

>=0.2.0

depends r-base:

>=4.3,<4.4.0a0

depends r-matrix:

>=1.2-12

depends r-pryr:

>=0.1.3

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-cagefightr

and update with::

   mamba update bioconductor-cagefightr

To create a new environment, run:

mamba create --name myenvname bioconductor-cagefightr

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-cagefightr:<tag>

(see `bioconductor-cagefightr/tags`_ for valid values for ``<tag>``)

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