recipe bioconductor-fishpond

Fishpond: downstream methods and tools for expression data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/fishpond.html

License:

GPL-2

Recipe:

/bioconductor-fishpond/meta.yaml

Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains a number of utilities for working with Salmon and Alevin quantification files.

package bioconductor-fishpond

versions:

2.8.0-0,  2.6.2-0,  2.4.0-0,  2.0.1-1,  2.0.1-0,  2.0.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0, 

2.8.0-0,  2.6.2-0,  2.4.0-0,  2.0.1-1,  2.0.1-0,  2.0.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.1-0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-qvalue:

>=2.34.0,<2.35.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-abind:

depends r-base:

>=4.3,<4.4.0a0

depends r-gtools:

depends r-jsonlite:

depends r-matrix:

depends r-matrixstats:

depends r-svmisc:

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-fishpond

and update with::

   mamba update bioconductor-fishpond

To create a new environment, run:

mamba create --name myenvname bioconductor-fishpond

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-fishpond:<tag>

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

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