yomix 1.4.0

yomix: an interactive tool to explore low dimensional embeddings of omics data

Yomix is an interactive tool to explore low dimensional embeddings of omics data.

INSTALL

In a python virtual environment, do:

pip install yomix

Then try the tool with:

yomix --example

To use it on your own files:

yomix yourfile.h5ad

where yourfile.h5ad is an anndata object saved in h5ad format (see anndata - Annotated data), with at least one .obsm field of dimension 2 or more.

When there are many samples in the dataset, the --subsampling option can be passed to improve reactiveness:

yomix --subsampling N yourfile.h5ad

It randomly subsamples the dataset to a maximum number of N samples. For example:

yomix --subsampling 5000 yourfile.h5ad

Other option: INSTALL FROM SOURCE

git clone https://github.com/perrin-isir/yomix.git

We recommand to create a python environment with micromamba, but any python package manager can be used instead.

cd yomix

micromamba create --name yomixenv --file environment.yaml

micromamba activate yomixenv

pip install -e .

Then try the tool with:

yomix yomix/example/pbmc.h5ad

The input file must be an anndata object saved in h5ad format (see anndata - Annotated data), with at least one .obsm field of dimension 2 or more.

List of contributors

Nicolas Perrin-Gilbert

Joshua Waterfall

Pierre Fumeron

Nisma Amjad

Jason Z. Kim

Erkan Narmanli

Christopher R. Myers

James P. Sethna

Jérôme Contant

Thomas Fuks

Julien Vibert