:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-tomoda' .. highlight: bash bioconductor-tomoda =================== .. conda:recipe:: bioconductor-tomoda :replaces_section_title: :noindex: Tomo\-seq data analysis :homepage: https://bioconductor.org/packages/3.18/bioc/html/tomoda.html :license: MIT + file LICENSE :recipe: /`bioconductor-tomoda `_/`meta.yaml `_ This package provides many easy\-to\-use methods to analyze and visualize tomo\-seq data. The tomo\-seq technique is based on cryosectioning of tissue and performing RNA\-seq on consecutive sections. \(Reference\: Kruse F\, Junker JP\, van Oudenaarden A\, Bakkers J. Tomo\-seq\: A method to obtain genome\-wide expression data with spatial resolution. Methods Cell Biol. 2016\;135\:299\-307. doi\:10.1016\/bs.mcb.2016.01.006\) The main purpose of the package is to find zones with similar transcriptional profiles and spatially expressed genes in a tomo\-seq sample. Several visulization functions are available to create easy\-to\-modify plots. .. conda:package:: bioconductor-tomoda |downloads_bioconductor-tomoda| |docker_bioconductor-tomoda| :versions: ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-1``,  ``1.0.0-0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-ggplot2: :depends r-ggrepel: :depends r-rcolorbrewer: :depends r-reshape2: :depends r-rtsne: :depends r-umap: :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-tomoda and update with:: mamba update bioconductor-tomoda To create a new environment, run:: mamba create --name myenvname bioconductor-tomoda 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-tomoda: (see `bioconductor-tomoda/tags`_ for valid values for ````) .. |downloads_bioconductor-tomoda| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-tomoda.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-tomoda :alt: (downloads) .. |docker_bioconductor-tomoda| image:: https://quay.io/repository/biocontainers/bioconductor-tomoda/status :target: https://quay.io/repository/biocontainers/bioconductor-tomoda .. _`bioconductor-tomoda/tags`: https://quay.io/repository/biocontainers/bioconductor-tomoda?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-tomoda/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-tomoda/README.html