- recipe bioconductor-ledpred
Learning from DNA to Predict Enhancers
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/LedPred.html
- License:
MIT | file LICENSE
- Recipe:
This package aims at creating a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, next-generation sequencing (NGS) peaks and signals and other numerical scores of the sequences using supervised classification. The package contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences, optimize SVM parameters and feature number and creates a model that can be stored and used to score the regulatory potential of unknown sequences.
- package bioconductor-ledpred¶
- Versions:
1.44.0-0,1.40.0-0,1.36.0-0,1.34.0-0,1.32.0-0,1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.44.0-0,1.40.0-0,1.36.0-0,1.34.0-0,1.32.0-0,1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.22.0-0,1.20.0-0,1.18.0-1,1.18.0-0,1.16.0-0- Depends:
on r-akima
on r-base
>=4.5,<4.6.0a0on r-e1071
>=1.6on r-ggplot2
on r-irr
on r-jsonlite
on r-plot3d
on r-plyr
on r-rcurl
on r-rocr
on r-testthat
- 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-ledpred
to add into an existing workspace instead, run:
pixi add bioconductor-ledpred
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-ledpred
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-ledpred
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-ledpred:<tag>
(see bioconductor-ledpred/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-ledpred/README.html)
