Witkop et al. 2023 Manuscript Code

This repository houses code used to analyze and generate figures from scRNA-seq and ATAC-seq data presented in Witkop et al., 2023.

ANALYSIS SCRIPTS

1. Scripts in the folders ATAC_Scripts_FIGURES_TABLES_RECREATE and scRNA_seq_scripts_FIGURES_TABLES_RECREATE should be referenced for directly making figures. Saved data objects and raw data referred to in each script are available for download via this box folder.
2. Scripts in the folders ATAC_Scripts_for_reference and scRNAseq_Scripts_for_reference should be used for referencing more complete code including additional analyses.

FIGURES AND TABLES KEY

The code used to generate each figure or table is presented below for each part of every figure (A, B, C, D, E, F). Code sections are labelled within each script for the figure or table they support.

FIGURES	A	B	C	D	E	F
Figure 1	Done in Inkscape	P452_3_T1DAL_Diffbind_Analysis_revised_FIGURES_TABLES_RECREATE.R	P452_3_T1DAL_Diffbind_Analysis_revised_FIGURES_TABLES_RECREATE.R	P452_3_T1DAL_Diffbind_Analysis_revised_FIGURES_TABLES_RECREATE.R	NA	NA
Figure 2	P452_3_T1DAL_Diffbind_Analysis_revised_FIGURES_TABLES_RECREATE.R	P452_3_T1DAL_Diffbind_Analysis_revised_FIGURES_TABLES_RECREATE.R	P452_3_T1DAL_Diffbind_Analysis_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA
Figure 3	Done in Inkscape	P362_1_T1DAL_10X_Compiled_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_10X_Compiled_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_Tex_signature_UMAPs_revised_FIGURES_TABLES_RECREATE.R	NA	NA
Figure 4	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	P452_3_HOMER_analysis_revised_FIGURES_TABLES_RECREATE.R	P452_3_HOMER_analysis_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA
Figure 5	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R
Figure 6	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	Done in Inkscape	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	NA	NA

SUPPLEMENTARY FIGURES	A	B	C	D	E	F
Figure S1	Done in flowjo and powerpoint	NA	NA	NA	NA	NA
Figure S2	P452_3_T1DAL_Diffbind_Analysis_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA	NA	NA
Figure S3	P452_3_T1DAL_Diffbind_Analysis_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA	NA	NA
Figure S4	Done in flowjo and powerpoint	NA	NA	NA	NA	NA
Figure S5	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_Multimodal_reference_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA
Figure S6	P362_1_T1DAL_pathology_association_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_pathology_association_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA	NA
Figure S7	P362_1_T1DAL_Tex_signature_UMAPs_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_Tex_signature_UMAPs_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA	NA
Figure S8	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA	NA	NA
Figure S9	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA
Figure S10	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA
Figure S11	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA	NA
Figure S12	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA	NA
Figure S13	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA	NA
Figure S14	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_TCR_Analysis_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA
Figure S15	P362_1_T1DAL_10X_Compiled_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_10X_Compiled_Analysis_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_Tex_signature_UMAPs_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_Tex_signature_UMAPs_revised_FIGURES_TABLES_RECREATE.R	NA	NA
Figure S16	P452_3_T1DAL_ATAC_seq_Comparison_revised_FIGURES_TABLES_RECREATE.R	P452_3_T1DAL_ATAC_seq_Comparison_revised_FIGURES_TABLES_RECREATE.R	P452_3_T1DAL_ATAC_seq_Comparison_revised_FIGURES_TABLES_RECREATE.R	P452_3_T1DAL_ATAC_seq_Comparison_revised_FIGURES_TABLES_RECREATE.R	P452_3_T1DAL_ATAC_seq_Comparison_revised_FIGURES_TABLES_RECREATE.R	NA

TABLES	A	B	C	D
Table S1	Compiled in word	NA	NA	NA
Table S2	P452_3_T1DAL_Diffbind_Analysis_revised_FIGURES_TABLES_RECREATE.R	P452_3_T1DAL_Diffbind_Analysis_revised_FIGURES_TABLES_RECREATE.R	P452_3_T1DAL_Diffbind_Analysis_revised_FIGURES_TABLES_RECREATE.R	P452_3_T1DAL_Diffbind_Analysis_revised_FIGURES_TABLES_RECREATE.R
Table S3	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R
Table S4	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	NA	NA
Table S5	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	NA	NA
Table S6	P452_3_HOMER_analysis_revised_FIGURES_TABLES_RECREATE.R	P452_3_HOMER_analysis_revised_FIGURES_TABLES_RECREATE.R	P452_3_HOMER_analysis_revised_FIGURES_TABLES_RECREATE.R	P452_3_HOMER_analysis_revised_FIGURES_TABLES_RECREATE.R
Table S7	P362_1_T1DAL_DGEA_revised_FIGURES_TABLES_RECREATE.R	NA	NA	NA