recipe bioconductor-tenxio

Import methods for 10X Genomics files

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-tenxio/meta.yaml

Provides a structured S4 approach to importing data files from the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene Expression data among other data types. The main Bioconductor data representations used are SingleCellExperiment and RaggedExperiment.

package bioconductor-tenxio

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocbaseutils:

>=1.4.0,<1.5.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocio:

>=1.12.0,<1.13.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-matrixgenerics:

>=1.14.0,<1.15.0

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-base:

>=4.3,<4.4.0a0

depends r-matrix:

depends r-r.utils:

depends r-rcurl:

depends r-readr:

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-tenxio

and update with::

   mamba update bioconductor-tenxio

To create a new environment, run:

mamba create --name myenvname bioconductor-tenxio

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-tenxio:<tag>

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

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