Welcome to tandem-genomics!

This project was conducted by Aymeric Degroote (@aymeric-degroote) & Matthieu Dagommer (@MatDagommer) as part of Statistical Machine Learning for Genomics (BMENE4480), supervised by Prof. Elham Azizi, Dpt. of Biomedical Engineering, Columbia University.

In this project, we combine two libraries, MultiVelo and CellRank, to simultaneously use RNA-seq and ATAC-seq data for cell trajectory inference. We do this by enriching the way velocity maps, a core component of cell trajectory inference, are computed. Velocity maps indicate the direction in which a cell's transcriptomics is evolving in gene expression space. velocyto, the original velocity map framework used in CellRank, computes these maps based on gene expression (RNA-seq) and spliced/unspliced RNA ratios only, while MultiVelo adds chromatin accessibility (ATAC-seq) to the mix. By replacing velocyto with MultiVelo in the CellRank inference framework, we enrich the inference with chromatin accessibility when this data is available.

Why tandem? Because CellRank and MultiVelo work as a tandem! Also, "Velo" means "bicycle" in French so "MultiVelo" naturally designates a tandem...

Proposed pipeline:

Expected folder hierarchy:

.
|-- src
|   |-- notebook-multivelo.ipynb
|   |-- notebook-pathways.ipynb
|   |-- notebook-preprocess.ipynb
|   `-- notebook-tandem.ipynb
|-- plots
`-- data
    |-- outs
    |   |-- analysis
    |   |   `-- feature_linkage
    |   |       `-- feature_linkage.bedpe
    |   |-- filtered_feature_bc_matrix
    |   |   |-- barcodes.tsv.gz
    |   |   |-- features.tsv.gz
    |   |   `-- matrix.mtx.gz
    |   `-- peak_annotation.tsv
    |-- results
    |   |-- adata_atac_mouse_brain.h5ad
    |   |-- adata_rna_mouse_brain_analyzed.h5ad
    |   |-- adata_rna_mouse_brain.h5ad
    |   |-- GSEA_overlap_result_0.tsv
    |   |-- GSEA_overlap_result_1.tsv
    |   |-- GSEA_overlap_rna_0.tsv
    |   `-- GSEA_overlap_rna_1.tsv
    |-- seurat_wnn
    |   |-- nn_cells.txt
    |   |-- nn_dist.txt
    |   `-- nn_idx.txt
    |-- velocyto
    |   `-- 10X_multiome_mouse_brain.loom
    |-- cell_annotations.tsv
    `-- filtered_cells.txt

Notebooks should be executed in the following order:

1. notebook-preprocess.ipynb
2. notebook-multivelo.ipynb
3. notebook-tandem.ipynb
4. notebook-pathways.ipynb