Review_of_B_cell

Note

This repository hosts the codes and intermediate results used to produce the key results in our research article, "Single-cell analysis reveals multi-faceted features of B cell development together with age-associated B cell subpopulations".

Table of contents

• Introduction of the codes
• Introduction of the intermediate results

Introduction of the codes

We organize our codes (either R or Python script) according to their applications. Generally, they fall into the following six categories,

1. Data preprocessing and cell population identification

   • RScript: DoubletFinder
   • RScript: Primary clustering & B cell secondary clustering

2. Gene regulation dynamics

   • Python: scVelo analysis

3. Trajectory inference

   • RScript: Monocle2 analysis

4. BCR repertoire analysis

   • Python: BCR repertoire analysis

5. Cell communication analysis

   • Python: CellPhoneDb analysis

6. External data investigation

   • Rscript: Import data and preprocessing
   • Python: Customized scripts

Introduction of the intermediate results

The following intermediate results can be used with the released codes to reproduce the key results in this study.

• CellPhoneDB.tar.gz: It stores all CCI prediction results generated by CellPhoneDB. CCI prediction in different tissue sources are seperately curated.
• IgBLAST_parsed_combined.txt.gz: This file records updated gene assignment information for BCR contigs. Exact V/D/J allele assignment was made for each contig for determination of SHM frequency.
• adata_merge_obs_metadata.csv.gz: This file stores cell metadata with velocity-based pseudotime prediction.
• bc.proj.clean.clone.csv.gz: This file stores assembled clonotype information for B cells in this study.
• bc.proj.clean.metadata.csv.gz: This file stores cell metadata.
• external_project_metadata.tar.gz: It stores the cell metadata information for 6 external single-cell studies. Expression levels of genes of interest are also precomputed.
• merged_filtered_contig_annotations_preprocessed.csv.gz: This file stores the annotation of BCR contigs from all in-house enriched B cell samples. BCR contigs were preprocessed to retain only one valid heavy chain contig and one valid light chain contig for each cell.
• rank_velocity_genes.csv: This file stores genes with top velocity score for each B cell subpopulation.

Others

If you have any questions related to these codes, please contact the authors through the following emails ([email protected], [email protected]).