:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-lymphoseq' .. highlight: bash bioconductor-lymphoseq ====================== .. conda:recipe:: bioconductor-lymphoseq :replaces_section_title: :noindex: Analyze high\-throughput sequencing of T and B cell receptors :homepage: https://bioconductor.org/packages/3.18/bioc/html/LymphoSeq.html :license: Artistic-2.0 :recipe: /`bioconductor-lymphoseq `_/`meta.yaml `_ 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. .. conda:package:: bioconductor-lymphoseq |downloads_bioconductor-lymphoseq| |docker_bioconductor-lymphoseq| :versions: .. raw:: html
1.30.0-01.28.0-01.26.0-01.22.0-01.20.0-01.18.0-11.18.0-01.16.0-01.14.0-0 ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.10.0-0`` .. raw:: html
:depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-ggtree: ``>=3.10.0,<3.11.0`` :depends bioconductor-lymphoseqdb: ``>=0.99.0,<0.100.0`` :depends bioconductor-msa: ``>=1.34.0,<1.35.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :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: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 quay.io/biocontainers/bioconductor-lymphoseq: (see `bioconductor-lymphoseq/tags`_ for valid values for ````) .. |downloads_bioconductor-lymphoseq| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-lymphoseq.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-lymphoseq :alt: (downloads) .. |docker_bioconductor-lymphoseq| image:: https://quay.io/repository/biocontainers/bioconductor-lymphoseq/status :target: https://quay.io/repository/biocontainers/bioconductor-lymphoseq .. _`bioconductor-lymphoseq/tags`: https://quay.io/repository/biocontainers/bioconductor-lymphoseq?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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-lymphoseq/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-lymphoseq/README.html