scRNAseq-scgem-nhdp

Libraries

• Seurat
• magrittr
• dplyr
• tibble
• msigdbr
• harmony
• biomaRt
• clusterProfiler
• org.Hs.eg.db
• lsa

Run run_pbmc3k to understand the Seurat workflow on sample PBMC data

Training

Use utils to split data (for easy computing only), add cell annotations, merge the final data together, and split the data according to cell type. Also use essential functions from utils.

Run training to train the nHDP model on single-cell data

Running Inference

Use a different single-cell dataset to infer with the trained model

Script for inference can be found here

Analyse inferred data with analyse_lc_tnk_inferred_data script

Analyse training data with analyse_crc_tnk_data script

Create UMAP plots using Seurat with tnk_plots script

Final findings can be found in the report