recipe bioconductor-transmogr

Modify a set of reference sequences using a set of variants

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-transmogr/meta.yaml

transmogR provides the tools needed to crate a new reference genome or reference transcriptome, using a set of variants. Variants can be any combination of SNPs, Insertions and Deletions. The intended use-case is to enable creation of variant-modified reference transcriptomes for incorporation into transcriptomic pseudo-alignment workflows, such as salmon.

package bioconductor-transmogr

versions:

1.2.0-0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-bsgenome:

>=1.74.0,<1.75.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicfeatures:

>=1.58.0,<1.59.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-variantannotation:

>=1.52.0,<1.53.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-ggplot2:

>=3.5.0

depends r-jsonlite:

depends r-matrixstats:

depends r-rlang:

depends r-scales:

depends r-vroom:

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-transmogr

and update with::

   mamba update bioconductor-transmogr

To create a new environment, run:

mamba create --name myenvname bioconductor-transmogr

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-transmogr:<tag>

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

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