recipe bioconductor-clustirr

Clustering of immune receptor repertoires

Homepage:

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

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-clustirr/meta.yaml

ClustIRR is a quantitative method for clustering of immune receptor repertoires (IRRs). The algorithm identifies groups of T or B cell receptors (TCRs or BCRs) with similar specificity by comparing their sequences. ClustIRR uses graphs to visualize the specificity structures of IRRs.

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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