Package Recipe 'bioconductor-clustirr'

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:

1.8.0-0, 1.4.0-0, 1.0.0-0

Depends:

on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-bh >=1.66.0
on r-blaster
on r-dplyr
on r-future
on r-future.apply
on r-ggforce
on r-ggplot2
on r-igraph
on r-posterior
on r-rcpp >=0.12.0
on r-rcppeigen >=0.3.3.3.0
on r-rcppparallel >=5.0.1
on r-reshape2
on r-rstan >=2.18.1
on r-rstantools >=2.4.0
on r-scales
on r-stanheaders >=2.18.0
on r-stringdist
on r-tidyr
on r-visnetwork
on tbb-devel >=2022.3.0,<2022.4.0a0

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-clustirr

to add into an existing workspace instead, run:

pixi add bioconductor-clustirr

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-clustirr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-clustirr

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-clustirr:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-clustirr/README.html)