diff --git a/README.md b/README.md index 94ac4f8..e7ed642 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,11 @@ -# Dissecting the cellular architecture of neuroblastoma bone marrow metastasis using single-cell transcriptomics and epigenomics unravels the role of monocytes at the metastatic niche +# Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7867892.svg)](https://doi.org/10.5281/zenodo.7867892) +This code supplements the [publication](https://doi.org/10.1038/s41467-023-39210-0) by Fetahu, Esser-Skala, Dnyansagar et al (2023). + + + ## Folders (Not all of these folders appear in the git repository.) @@ -111,7 +115,7 @@ All required scripts are in subfolder `scatac`. ### scATAC-seq workflow - [R0_scopen.R](scatac/R0_scopen.R) – - quality control, normalization, clustering + quality control, normalization, clustering - [R1_annotation.R](scatac/R1_annotation.R) – annotation of clusters formed and markers used - [R2_foot_printing_cell_type.R](scatac/R2_foot_printing_cell_type.R) – @@ -134,13 +138,13 @@ All required scripts are in subfolder `scatac`. For data integration we used scGLUE (Graph Linked Unified Embedding) model for unpaired single-cell multi-omics data integration (https://scglue.readthedocs.io/en/latest/). We followed the detailed tutorial at https://scglue.readthedocs.io/en/latest/tutorials.html. Before the tutorial we needed to convert the objects in anndata format from SingleCellExperiment and Seurat for scRNA-seq and scATAC-seq respectively. There are many tools available to do this and we are sharing our approach for format conversion, namely [monocle_to_anndata.R](scatac/monocle_to_anndata.R) and [Seurat_to_anndata.R](scatac/Seurat_to_anndata.R). -The following Jupyter notebooks follow the notebooks of the scGLUE integration pipeline. +The following Jupyter notebooks follow the notebooks of the scGLUE integration pipeline. - [G1_nb_glue_preprocessing_myeloid.ipynb]() – preprocess scRNA-seq and scATAC-seq anndata objects - [G2_glue_model_myeloid.ipynb]() – - create glue model -- [G3_regulatory_inference_myeloid.ipynb]() + create glue model +- [G3_regulatory_inference_myeloid.ipynb]() - [G4_regulatory_network_plots_myeloid.ipynb]() -Finally, [Figures.R](scatac/Figures.R) generates publication figures. \ No newline at end of file +Finally, [Figures.R](scatac/Figures.R) generates publication figures.