Toxoplasma_CDC

Toxoplasma_CDC

prepScOutPut.R - process the output of cellranger

1. readProcScRNA.R - read and process raw rna expression (counts)

2. readProcScATAC.R - read and process raw atac profile (counts)

3. peak_gene_assignment_scATAC.R

4. marker_analysis.R

perform marker analysis on the following:

1. rna markers using phase as Idents
2. rna markers using rna transition points as Idents
3. rna markers using atac transition points as Idesnts

note: Intersection of 2 & 3 is in this code

7. fitPseudoTime_scATAC_scRNA_V2.R - fit pseudo-time to scRNA and scATAC

8. sc_rna_sc_atac_fit_smoothing_splines.R - fitting smoothing splines to scRNA and scATAC

9. scRNA_scATAC_correlation_analysis.R - correlation analysis between expr and atac curves

10. map_transition_final.R - Infer transition in peak expression and peak accessibility during

AP2XII-8 KD

9. readProcScRNA_AP2XII8_transfer_labels.R - Read and process AP2XII-8 scRNA KD

10. integration_V2.R - integrates WT and KD seurat objects

11. all types of DEGs between KD and WT - integratedMarkerAnalysis.R

note: Here I used the integrated objects because for finding markers seurat function only accepts one single object. However, when we set the assay to RNA it ignores integration.

11. Cut&RUN on AP2XII-8 KD - CutRun_MArch_automated_No_frag_filt.R

peak_gene assignment on individual narrow peaks peak_gene assignment on union of 4 data moif occurence public chip information

12. Cut_run_March_exploratory_final.R - Cut&run and DEGs (KD_vs_WT) exploratory analysis

note: all figures and tables for downstream analysis of cut&run and DEGs(KD_vs_WT) has been done in this script. PowerPoint CutRUN_DEGs_V4_05_05_23 analysis

13. Dynamic time Warping clustering of gene sets - dtw_clustering_rna_tran_new.R This script takes genes and cluster them and plot the rna and atac profiles according to the cluster. (ordered rna clusters)

14. Dynamic time Warping clustering of gene sets - dtw_clusters_cutRun_DEGs_new.R

15. all_expression_atac_profiles.R

If we dont want to cluster the expression or accessibility curves, we can use this script to plot the expression and accessibility of a gene set.

15. GO_enrichment_new.R

takes the output of toxodb enrichment analsys process the tables and plot the top rankes GO terms.

16. sc_expr_plot.R - plots rna expression of KD and WT + violin plots for each each gene

17. heatmaps_trans.R - generates heatmap of expression of cell cycle regulated genes ordered by rna peak time

18. heatmaps_trans_order_by_atac.R generates heatmap of expression of cell cycle regulated genes ordered by atac peak time

19. AP2_clustering.R

Clusters cyclic AP2s (new from the review paper)

20. IMCs_clusters.R, BCs_clustersR

cluster new list of BC and IMC genes

21. circosPlot_app.r plots the circos for gene families the rds file has been generated in circosPlot.r

22. plot_trends.r

plots the expression and atac profile of each gene one at a time