recipe bioconductor-lymphoseq

Analyze high-throughput sequencing of T and B cell receptors






This R package analyzes high-throughput sequencing of T and B cell receptor complementarity determining region 3 (CDR3) sequences generated by Adaptive Biotechnologies' ImmunoSEQ assay. Its input comes from tab-separated value (.tsv) files exported from the ImmunoSEQ analyzer.

package bioconductor-lymphoseq

(downloads) docker_bioconductor-lymphoseq



depends bioconductor-biostrings:


depends bioconductor-ggtree:


depends bioconductor-lymphoseqdb:


depends bioconductor-msa:


depends r-base:


depends r-circlize:

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-ineq:

depends r-phangorn:

depends r-plyr:

depends r-rcolorbrewer:

depends r-reshape:

depends r-stringdist:

depends r-upsetr:

depends r-venndiagram:



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-lymphoseq

and update with::

   mamba update bioconductor-lymphoseq

To create a new environment, run:

mamba create --name myenvname bioconductor-lymphoseq

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<tag>

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

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