HCMI_snRNAseq_data_metadata

Collection of data and metadata for running snRNA-seq demo codes at Califano Lab Github: HCMI Demo Codes. (Directories in bold).demultiplexed_samples_best_gt_thresh-filtered-01/: Directory containing .h5ad files for demultiplexed samples.metadata/: Metadata tables for each demultiplexed sample, including standard gene expression analyses and infercnv outputs.clustering/: Directory containing optimal Leiden clustering parameters identified using acdcPAAD_networks/: Gene regulatory networks used for protein activity analysis of pancreatic samples in Figure-5e-5f-5g-Extended-Data-Figure-7b-7e.ipynbGBM-networks/: Gene regulatory network used for protein activity-based PCA projection of GBM samples in Figure-5b-5c.ipynbprotein_activity_metadata_ref_cells_from_model/: directory collecting additional metadata from protein activitity analyses, e.g., PAAD transcriptional state annotation.PDAC-all-samples-protein-activity-ref-cells_from_model-NES.tsv: VIPER-inferred protein activity matrix for malignant cells across all PAAD snRNA-seq samples, used in Figure-5e-5f-5g-Extended-Data-Figure-7b-7e.ipynb.(Note: the suffix indicates that the protein activity matrix was generated with respect to a reference set of nuclei from models, but the matrix includes samples from both tumors and models.)PDAC-all-samples-ref-cells_from_model-PCA.csv: PCA coordinates for protein activity visualization of PAAD samples, used in 5e-5f-5g-Extended-Data-Figure-7b-7e.ipynbGBM-malignant-reference-signature.tsv: Gene statistics computed from the reference cell population used for data centering and scaling in Figure-5b-5c.ipynb and Figure-5d.ipynb