- recipe bioconductor-scfa
SCFA: Subtyping via Consensus Factor Analysis
- Homepage:
- License:
LGPL
- Recipe:
Subtyping via Consensus Factor Analysis (SCFA) can efficiently remove noisy signals from consistent molecular patterns in multi-omics data. SCFA first uses an autoencoder to select only important features and then repeatedly performs factor analysis to represent the data with different numbers of factors. Using these representations, it can reliably identify cancer subtypes and accurately predict risk scores of patients.
- package bioconductor-scfa¶
- Versions:
1.20.0-0,1.16.0-0,1.12.0-0,1.10.0-0,1.8.0-0,1.4.0-0,1.2.0-0,1.0.0-1,1.0.0-0- Depends:
on bioconductor-biocparallel
>=1.44.0,<1.45.0on r-base
>=4.5,<4.6.0a0on r-cluster
on r-coro
on r-glmnet
on r-igraph
on r-matrix
on r-matrixstats
on r-psych
on r-rhpcblasctl
on r-survival
on r-torch
>=0.3.0
- 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-scfa
to add into an existing workspace instead, run:
pixi add bioconductor-scfa
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-scfa
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-scfa
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-scfa:<tag>
(see bioconductor-scfa/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-scfa/README.html)
