recipe bioconductor-dasper

Detecting abberant splicing events from RNA-sequencing data

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-dasper/meta.yaml

The aim of dasper is to detect aberrant splicing events from RNA-seq data. dasper will use as input both junction and coverage data from RNA-seq to calculate the deviation of each splicing event in a patient from a set of user-defined controls. dasper uses an unsupervised outlier detection algorithm to score each splicing event in the patient with an outlier score representing the degree to which that splicing event looks abnormal.

package bioconductor-dasper

versions:

1.9.0-0,  1.7.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-2,  1.0.0-1

depends bioconductor-basilisk:

>=1.12.0,<1.13.0

depends bioconductor-biocfilecache:

>=2.8.0,<2.9.0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-megadepth:

>=1.10.0,<1.11.0

depends bioconductor-plyranges:

>=1.20.0,<1.21.0

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-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-ggpubr:

depends r-ggrepel:

depends r-magrittr:

depends r-readr:

depends r-reticulate:

depends r-stringr:

depends r-tidyr:

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-dasper

and update with::

   mamba update bioconductor-dasper

To create a new environment, run:

mamba create --name myenvname bioconductor-dasper

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-dasper:<tag>

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

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