analysis scripts in the Ng et al. sciCSR paper.
| filename | Description | Relevant figure(s) |
|---|---|---|
folder simulation |
Bash code used to process simulated IgH reads | Figure 2b,c |
plotBedGraphs.Rmd |
plotting distribution of reads & motifs across IgH locus | Figure 2a, Supplementary Figures S1, S2 |
simulate_IGHC_reads.Rmd |
Code to simulate RNA-seq reads from IgH transcripts and analysis | Figure 2b,c |
human_atlas.Rmd |
Code to assemble reference atlas for human B cells, visualisation of productive/sterile transcription, derivation of isotype signatures | Figure 2d, 4a, 4b, Supplementary Figure S3, S5, S6, S7 |
scIFNg_sciCSR.Rmd |
Code to analyse the interferon gamma culture scRNA-seq/scBCR-seq data | Figure 3 |
Kim_Covid_GLT.Rmd |
Code to analyse the SARS-CoV-2 vaccination time-course (Kim et al. Nature 2022) data | Figure 5, Supplementary Figure S4, S8 |
Gomez_AID.Rmd |
Code to analyse the Aicda mouse knockout (Gómez-Escolar et al. EMBO Rep 2022) data | Figure 6a,b |
Hong_IL23_GLT.Rmd |
Code to analyse the Il23 mouse knockout (Hong et al. J Immunol 2020) data | Figure 6a,c-f, Supplementary Figure S9 |
simulated_transitions.Rmd |
Code to assess the effect of dataset size on sciCSR inference | Supplementary Note 1 |