:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-sagenhaft' .. highlight: bash bioconductor-sagenhaft ====================== .. conda:recipe:: bioconductor-sagenhaft :replaces_section_title: :noindex: Collection of functions for reading and comparing SAGE libraries :homepage: https://bioconductor.org/packages/3.18/bioc/html/sagenhaft.html :license: GPL (>= 2) :recipe: /`bioconductor-sagenhaft `_/`meta.yaml `_ :links: biotools: :biotools:`sagenhaft`, doi: :doi:`10.1038/nmeth.3252` This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE \(Serial Analysis of Gene Expressen\) data\, i.e. extraction of a SAGE library from sequence files\, sequence error correction\, library comparison. Sequencing error correction is implementing using an Expectation Maximization Algorithm based on a Mixture Model of tag counts. .. conda:package:: bioconductor-sagenhaft |downloads_bioconductor-sagenhaft| |docker_bioconductor-sagenhaft| :versions: .. raw:: html
1.72.0-11.72.0-01.70.0-01.68.0-01.64.0-01.62.0-01.60.0-11.60.0-01.58.0-0 ``1.72.0-1``,  ``1.72.0-0``,  ``1.70.0-0``,  ``1.68.0-0``,  ``1.64.0-0``,  ``1.62.0-0``,  ``1.60.0-1``,  ``1.60.0-0``,  ``1.58.0-0``,  ``1.56.0-0``,  ``1.54.0-1``,  ``1.54.0-0``,  ``1.52.0-0``,  ``1.50.0-0``,  ``1.48.0-0``,  ``1.46.0-0`` .. raw:: html
:depends r-base: ``>=4.3,<4.4.0a0`` :depends r-sparsem: ``>=0.73`` :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-sagenhaft and update with:: mamba update bioconductor-sagenhaft To create a new environment, run:: mamba create --name myenvname bioconductor-sagenhaft 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-sagenhaft: (see `bioconductor-sagenhaft/tags`_ for valid values for ````) .. |downloads_bioconductor-sagenhaft| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-sagenhaft.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-sagenhaft :alt: (downloads) .. |docker_bioconductor-sagenhaft| image:: https://quay.io/repository/biocontainers/bioconductor-sagenhaft/status :target: https://quay.io/repository/biocontainers/bioconductor-sagenhaft .. _`bioconductor-sagenhaft/tags`: https://quay.io/repository/biocontainers/bioconductor-sagenhaft?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-sagenhaft/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-sagenhaft/README.html