recipe bioconductor-multtest

Resampling-based multiple hypothesis testing

Homepage:

https://bioconductor.org/packages/3.16/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:

2.54.0-1,  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, 

2.54.0-1,  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 >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• r-base >=4.2,<4.3.0a0

• r-mass

• r-survival

Required By:

• bioconductor-anota

• bioconductor-anota2seq

• bioconductor-adsplit

• bioconductor-preda

• bioconductor-synapter

• bioconductor-phyloseq

• bioconductor-redseq

• bioconductor-acgh

• bioconductor-bicare

• bioconductor-a4base

• bioconductor-rtopper

• bioconductor-chippeakanno

• bioconductor-singlecelltk

• bioconductor-metabomxtr

• bioconductor-aldex2

• bioconductor-microbiomemarker

• bioconductor-rain

• bioconductor-nethet

• bioconductor-kcsmart

• bioconductor-webbioc

• bioconductor-abarray

• seurat-scripts

• bioconductor-mapkl

• bioconductor-guideseq

• bioconductor-ocplus

• bioconductor-singlecellsignalr

• r-mutoss

• r-diffcorr

• r-structssi

• bioconductor-ipac

• r-cp4p

• bioconductor-siggenes

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-multtest

and update with:

conda update bioconductor-multtest

or 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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