recipe bioconductor-ancombc

Microbiome differential abudance and correlation analyses with bias correction

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/ANCOMBC.html

License:

Artistic-2.0

Recipe:

/bioconductor-ancombc/meta.yaml

ANCOMBC is a package containing differential abundance (DA) and correlation analyses for microbiome data. Specifically, the package includes Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2), Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), and Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse Estimation of Correlations among Microbiomes (SECOM) for correlation analysis. Microbiome data are typically subject to two sources of biases: unequal sampling fractions (sample-specific biases) and differential sequencing efficiencies (taxon-specific biases). Methodologies included in the ANCOMBC package are designed to correct these biases and construct statistically consistent estimators.

package bioconductor-ancombc

Versions:

2.0.1-0,  1.4.0-0,  1.2.0-0,  1.0.5-0,  1.0.0-2

Depends:

• bioconductor-mia >=1.6.0,<1.7.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• bioconductor-treesummarizedexperiment >=2.6.0,<2.7.0

• r-base >=4.2,<4.3.0a0

• r-cvxr

• r-desctools

• r-doparallel

• r-dorng

• r-dplyr

• r-emmeans

• r-energy

• r-foreach

• r-hmisc

• r-lme4

• r-lmertest

• r-magrittr

• r-mass

• r-nloptr

• r-rdpack

• r-rlang

• r-rngtools

• r-tibble

• r-tidyr

Required By:

• bioconductor-benchdamic

• bioconductor-microbiomemarker

Installation

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

conda install bioconductor-ancombc

and update with:

conda update bioconductor-ancombc

or use the docker container:

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

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

Download stats

Link to this page

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