recipe bioconductor-primirtss

Prediction of pri-miRNA Transcription Start Site

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/primirTSS.html

License:

GPL-2

Recipe:

/bioconductor-primirtss/meta.yaml

A fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs.

package bioconductor-primirtss

versions:

1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0, 

1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-1,  1.0.1-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-bsgenome.hsapiens.ucsc.hg38:

>=1.4.0,<1.5.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-genomicscores:

>=2.18.0,<2.19.0

depends bioconductor-gviz:

>=1.50.0,<1.51.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-jaspar2018:

>=1.1.0,<1.2.0

depends bioconductor-phastcons100way.ucsc.hg38:

>=3.7.0,<3.8.0

depends bioconductor-rtracklayer:

>=1.66.0,<1.67.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-tfbstools:

>=1.44.0,<1.45.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

>=0.7.6

depends r-purrr:

>=0.2.5

depends r-r.utils:

>=2.6.0

depends r-shiny:

>=1.0.5

depends r-stringr:

>=1.3.1

depends r-tibble:

>=1.4.2

depends r-tidyr:

>=0.8.1

requirements:

additional platforms:

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-primirtss

and update with::

   mamba update bioconductor-primirtss

To create a new environment, run:

mamba create --name myenvname bioconductor-primirtss

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-primirtss:<tag>

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

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