2021_NI_scGCB

This repository contains some scripts used for our Nature Immunology paper entitled "Coupled analysis of transcriptome and BCR mutations reveals role of OXPHOS in affinity maturation", including:

• script:

  • GCB_NP.Rmd: Classical analysis of scRNA-seq data of NP-specific GC B cells
  • Signature_score.Rmd: Signature score calculation based on gene list
  • Topic_model.Rmd: Topic modeling analysis of scRNA-seq data
  • Igblast_parsing.Rmd: Detailed code for parsing output of CellRanger VDJ and IgBlast
  • BCR.Rmd: Combine BCR (affinity) info with scRNA-seq to identify difference between high- and low-affinity groups
  • monocle2.R: Pseudotime analysis using Monocle 2

• html: Corresponding html output of .Rmd file in directory script