recipe bioconductor-multtest

Resampling-based multiple hypothesis testing

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/multtest.html

License:

LGPL-3-only

Recipe:

/bioconductor-multtest/meta.yaml

Links:

biotools: multtest, 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.

package bioconductor-multtest

versions:

2.58.0-1,  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, 

2.58.0-1,  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

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:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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:<tag>

(see `bioconductor-multtest/tags`_ for valid values for ``<tag>``)

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