recipe bioconductor-circrnaprofiler

circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/circRNAprofiler.html

License:

GPL-3

Recipe:

/bioconductor-circrnaprofiler/meta.yaml

R-based computational framework for a comprehensive in silico analysis of circRNAs. This computational framework allows to combine and analyze circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.

package bioconductor-circrnaprofiler

versions:

1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.2-0,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-annotationhub:

>=3.8.0,<3.9.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-bsgenome:

>=1.68.0,<1.69.0

depends bioconductor-bsgenome.hsapiens.ucsc.hg19:

>=1.4.0,<1.5.0

depends bioconductor-deseq2:

>=1.40.0,<1.41.0

depends bioconductor-edger:

>=3.42.0,<3.43.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-gwascat:

>=2.32.0,<2.33.0

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-universalmotif:

>=1.18.0,<1.19.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-magrittr:

depends r-r.utils:

depends r-readr:

depends r-reshape2:

depends r-rlang:

depends r-seqinr:

depends r-stringi:

depends r-stringr:

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-circrnaprofiler

and update with::

   mamba update bioconductor-circrnaprofiler

To create a new environment, run:

mamba create --name myenvname bioconductor-circrnaprofiler

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-circrnaprofiler:<tag>

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

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