Package Recipe 'bioconductor-multtest'

recipe bioconductor-multtest

Resampling-based multiple hypothesis testing

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/multtest.html
License:: LGPL
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:

2.66.0-0, 2.62.0-1, 2.62.0-0, 2.58.0-1, 2.58.0-0, 2.56.0-0, 2.54.0-1, 2.54.0-0, 2.50.0-2,

2.66.0-0, 2.62.0-1, 2.62.0-0, 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:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biobase >=2.70.0,<2.71.0a0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-mass
on r-survival

Additional platforms:

linux-aarch64, osx-arm64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-multtest

to add into an existing workspace instead, run:

pixi add bioconductor-multtest

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-multtest

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-multtest

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-multtest:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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)