recipe bioconductor-clustirr

Clustering of immune receptor repertoires

Homepage:

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

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-clustirr/meta.yaml

ClustIRR analyzes repertoires of B- and T-cell receptors. It starts by identifying communities of immune receptors with similar specificities, based on the sequences of their complementarity-determining regions (CDRs). Next, it employs a Bayesian probabilistic models to quantify differential community occupancy (DCO) between repertoires, allowing the identification of expanding or contracting communities in response to e.g. infection or cancer treatment.

package bioconductor-clustirr

versions:

1.4.0-0,  1.0.0-0

depends bioconductor-pwalign:

>=1.2.0,<1.3.0

depends bioconductor-pwalign:

>=1.2.0,<1.3.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-bh:

>=1.66.0

depends r-blaster:

depends r-future:

depends r-future.apply:

depends r-igraph:

depends r-rcpp:

>=0.12.0

depends r-rcppeigen:

>=0.3.3.3.0

depends r-rcppparallel:

>=5.0.1

depends r-reshape2:

depends r-rstan:

>=2.18.1

depends r-rstantools:

>=2.4.0

depends r-stanheaders:

>=2.18.0

depends r-stringdist:

depends r-visnetwork:

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-clustirr

and update with::

   mamba update bioconductor-clustirr

To create a new environment, run:

mamba create --name myenvname bioconductor-clustirr

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-clustirr:<tag>

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

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