:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-tscan' .. highlight: bash bioconductor-tscan ================== .. conda:recipe:: bioconductor-tscan :replaces_section_title: :noindex: Tools for Single\-Cell Analysis :homepage: https://bioconductor.org/packages/3.18/bioc/html/TSCAN.html :license: GPL(>=2) :recipe: /`bioconductor-tscan `_/`meta.yaml `_ :links: biotools: :biotools:`tscan`, doi: :doi:`10.1093/nar/gkw430` Provides methods to perform trajectory analysis based on a minimum spanning tree constructed from cluster centroids. Computes pseudotemporal cell orderings by mapping cells in each cluster \(or new cells\) to the closest edge in the tree. Uses linear modelling to identify differentially expressed genes along each path through the tree. Several plotting and interactive visualization functions are also implemented. .. conda:package:: bioconductor-tscan |downloads_bioconductor-tscan| |docker_bioconductor-tscan| :versions: .. raw:: html
1.40.0-01.38.0-01.36.0-01.32.0-01.30.0-01.28.0-11.28.0-01.26.0-01.24.0-0 ``1.40.0-0``,  ``1.38.0-0``,  ``1.36.0-0``,  ``1.32.0-0``,  ``1.30.0-0``,  ``1.28.0-1``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0`` .. raw:: html
:depends bioconductor-delayedarray: ``>=0.28.0,<0.29.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-trajectoryutils: ``>=1.10.0,<1.11.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-combinat: :depends r-fastica: :depends r-ggplot2: :depends r-gplots: :depends r-igraph: :depends r-matrix: :depends r-mclust: :depends r-mgcv: :depends r-plyr: :depends r-shiny: :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-tscan and update with:: mamba update bioconductor-tscan To create a new environment, run:: mamba create --name myenvname bioconductor-tscan 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-tscan: (see `bioconductor-tscan/tags`_ for valid values for ````) .. |downloads_bioconductor-tscan| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-tscan.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-tscan :alt: (downloads) .. |docker_bioconductor-tscan| image:: https://quay.io/repository/biocontainers/bioconductor-tscan/status :target: https://quay.io/repository/biocontainers/bioconductor-tscan .. _`bioconductor-tscan/tags`: https://quay.io/repository/biocontainers/bioconductor-tscan?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-tscan/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-tscan/README.html