- recipe bioconductor-ancombc
Microbiome differential abudance and correlation analyses with bias correction
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/ANCOMBC.html
- License:
Artistic-2.0
- Recipe:
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:
2.12.0-0,2.8.0-0,2.4.0-0,2.2.0-0,2.0.1-0,1.4.0-0,1.2.0-0,1.0.5-0,1.0.0-2- Depends:
on r-base
>=4.5,<4.6.0a0on r-cvxr
on r-desctools
on r-doparallel
on r-dorng
on r-energy
on r-foreach
on r-gtools
on r-hmisc
on r-lme4
on r-lmertest
on r-mass
on r-matrix
on r-multcomp
on r-nloptr
on r-rdpack
- Additional platforms:
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-ancombc
to add into an existing workspace instead, run:
pixi add bioconductor-ancombc
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-ancombc
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-ancombc
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-ancombc:<tag>
(see bioconductor-ancombc/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:
[](http://bioconda.github.io/recipes/bioconductor-ancombc/README.html)
