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cite-seq_optimization

Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments

ctcl_kc_sa_presentation

Code used in analysis for the article "Keratinocytes present Staphylococcus aureus enterotoxins and promote malignant and non-malignant T cell proliferation in cutaneous T cell lymphoma"

ctcl_se_drug_resistance

fcutility

Utility functions for working with Flow Cytometry data in R

multisce

Package for loading and separating multiple (alternative) experiments into smaller elements to provide more flexibility in loading and saving large highly multi-modal datasets

numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

scfeaturerank

Feature Rank plot for single-cell analysis (developed for evaluation of (EC)CITE-seq optimizations).

scutility

Utility functions for scRNA-seq focused on ECCITE-seq analysis

scvdj

Package for analyzing VDJ (T-/B-cell receptor) clones in single-cell data