Pipeline and miscellaneous scripts for processing CTCL ECCITE-seq data

The pipeline was created using Snakemake

Software Pre-requisites

• 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