The pipeline was created using Snakemake
- Cell Ranger (v 3.0.1) - Process 10X 5' GEX and VDJ data for alignment, cell barcode identification, read de-duplication using UMI barcodes, tabulation gene counts and clonotype assembly
- CITE-seq-Count (v 1.3.2) - Pre-processing of ADT and HTO data
- Seurat (v 3.0.1) - Downstream single cell analyses
- HTODemux - Addition function under the Seurat package to demultiplex pooled samples based on the their assigned HTO barcode
- Scrublet (v 0.2.1) - Intra-sample doublet detection
- JointVis (v 0.1) - Multi-modal joint analysis using network fusion techniques