- recipe flexynesis
A deep-learning-based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.
- Homepage:
- Documentation:
https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis/site/getting_started
- License:
OTHER
- Recipe:
This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.
- package flexynesis¶
- Versions:
1.1.7-0,1.1.6-0,1.1.5-0,1.1.4-0,1.1.3-1,1.1.3-0,1.1.1-0,1.1.0-0,1.0.8-0,1.1.7-0,1.1.6-0,1.1.5-0,1.1.4-0,1.1.3-1,1.1.3-0,1.1.1-0,1.1.0-0,1.0.8-0,1.0.7-0,1.0.5-0,1.0.4-0,1.0.3-0,0.2.20-0,0.2.19-0,0.2.18-0,0.2.17-0,0.2.16-0,0.2.14-0,0.2.13-0,0.2.12-0,0.2.11-0,0.2.10-0- Depends:
on captum
on geomloss
on ipykernel
on ipywidgets
on lifelines
on lightning
on matplotlib-base
on numpy
on pandas
on papermill
on plotnine
on pot
on python
>=3.11on python-louvain
on pytorch
on pytorch_geometric
on pyyaml
on rich
on safetensors
on scikit-optimize
on scikit-survival
on scipy
on seaborn-base
on torchvision
on tqdm
on umap-learn
on xgboost
- 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 flexynesis
to add into an existing workspace instead, run:
pixi add flexynesis
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 flexynesis
Alternatively, to install into a new environment, run:
conda create -n envname flexynesis
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/flexynesis:<tag>
(see flexynesis/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/flexynesis/README.html)
