multivelo 0.1.5

Installation

Install through PyPI:

pip install multivelo

The package is also available on Bioconda. Install with:

conda install -c bioconda multivelo or mamba install -c bioconda multivelo

Documentation

We have a ReadTheDocs page.

Tutorial

New: we have added Jupyter notebooks showing how to reproduce the main figure panels, along with all required processed data files. These can be found under the Examples folder in this repository or on our ReadTheDocs page.

A tutorial showing how to run MultiVelo can be found here: (jupyter notebook)

The tutorial uses the embryonic E18 mouse brain from 10X Multiome as an example. CellRanger output files can be downloaded from 10X website. Crucially, the filtered feature barcode matrix folder, ATAC peak annotations TSV, and the feature linkage BEDPE file in the secondary analysis outputs folder will be needed in this demo.

You can download the processed data that we used for this analysis if you want to run the example yourself. Unspliced and spliced counts, as well as cell type annotations can be downloaded from the MultiVelo GitHub page. We provide the cell annotations for this dataset in “cell_annotations.tsv”. We also provide the nearest neighbor graph used to smooth chromatin accessibility values in the GitHub folder “seurat_wnn”, which contains a zip file of three files: “nn_cells.txt”, “nn_dist.txt”, and “nn_idx.txt”. Please unzip the archive after downloading. The R script used to generate these files can also be found in the same folder.

Citation