:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-multtest' .. highlight: bash bioconductor-multtest ===================== .. conda:recipe:: bioconductor-multtest :replaces_section_title: :noindex: Resampling\-based multiple hypothesis testing :homepage: https://bioconductor.org/packages/3.18/bioc/html/multtest.html :license: LGPL :recipe: /`bioconductor-multtest `_/`meta.yaml `_ :links: biotools: :biotools:`multtest`, doi: :doi:`10.1007/0-387-29362-0_15` Non\-parametric bootstrap and permutation resampling\-based multiple testing procedures \(including empirical Bayes methods\) for controlling the family\-wise error rate \(FWER\)\, generalized family\-wise error rate \(gFWER\)\, tail probability of the proportion of false positives \(TPPFP\)\, and false discovery rate \(FDR\). Several choices of bootstrap\-based null distribution are implemented \(centered\, centered and scaled\, quantile\-transformed\). Single\-step and step\-wise methods are available. Tests based on a variety of t\- and F\-statistics \(including t\-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters\) are included. When probing hypotheses with t\-statistics\, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p\-values\, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments. .. conda:package:: bioconductor-multtest |downloads_bioconductor-multtest| |docker_bioconductor-multtest| :versions: .. raw:: html
2.58.0-02.56.0-02.54.0-12.54.0-02.50.0-22.50.0-12.50.0-02.48.0-02.46.0-1 ``2.58.0-0``,  ``2.56.0-0``,  ``2.54.0-1``,  ``2.54.0-0``,  ``2.50.0-2``,  ``2.50.0-1``,  ``2.50.0-0``,  ``2.48.0-0``,  ``2.46.0-1``,  ``2.46.0-0``,  ``2.44.0-0``,  ``2.42.0-0``,  ``2.40.0-1``,  ``2.38.0-0``,  ``2.36.0-0``,  ``2.34.0-0``,  ``2.32.0-0``,  ``2.28.0-1``,  ``2.28.0-0``,  ``2.26.0-0`` .. raw:: html
:depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0a0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-mass: :depends r-survival: :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-multtest and update with:: mamba update bioconductor-multtest To create a new environment, run:: mamba create --name myenvname bioconductor-multtest 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-multtest: (see `bioconductor-multtest/tags`_ for valid values for ````) .. |downloads_bioconductor-multtest| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-multtest.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-multtest :alt: (downloads) .. |docker_bioconductor-multtest| image:: https://quay.io/repository/biocontainers/bioconductor-multtest/status :target: https://quay.io/repository/biocontainers/bioconductor-multtest .. _`bioconductor-multtest/tags`: https://quay.io/repository/biocontainers/bioconductor-multtest?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-multtest/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-multtest/README.html