recipe drop

Detection of RNA Outlier Pipeline

Homepage:

https://github.com/gagneurlab/drop

Documentation:

https://gagneurlab-drop.readthedocs.io/en/latest/

License:

OTHER / MIT

Recipe:

/drop/meta.yaml

Links:

https: :https:`//doi.org/10.1038/s41596-020-00462-5`

package drop

versions:

1.4.0-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.4-0,  1.2.3-0,  1.2.2-0, 

1.4.0-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.4-0,  1.2.3-0,  1.2.2-0,  1.2.1-0,  1.1.4-0,  1.1.3-0,  1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.5-0,  1.0.4-0,  1.0.3-1,  1.0.3-0,  1.0.2-0,  1.0.1-0,  1.0.0-0,  0.9.2-0,  0.9.1-0,  0.9.0-0

depends bc:

depends bcftools:

>=1.9

depends bioconductor-deseq2:

depends bioconductor-fraser:

>=1.99.4

depends bioconductor-genomicscores:

depends bioconductor-outrider:

>=1.20.1

depends bioconductor-variantannotation:

depends click:

>=7.0

depends click-log:

depends gatk4:

>=4.0.4

depends graphviz:

depends htslib:

depends pandas:

depends pandoc:

depends python:

>=3.6

depends python-dateutil:

depends r-base:

>=4.0.0

depends r-cowplot:

depends r-data.table:

depends r-devtools:

depends r-dplyr:

depends r-ggplot2:

depends r-ggthemes:

depends r-knitr:

depends r-magrittr:

depends r-rmarkdown:

depends r-tidyr:

depends r-tmae:

>=1.0.4

depends samtools:

>=1.9

depends snakemake-minimal:

>=5.5.2

depends star:

>=2.7

depends wbuild:

>=1.8 pyhdfd78af_2

depends wget:

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 drop

and update with::

   mamba update drop

To create a new environment, run:

mamba create --name myenvname drop

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/drop:<tag>

(see `drop/tags`_ for valid values for ``<tag>``)

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