Skip to content

List of all R codes used for the analysis of single cell data in the paper Blecher et al. on the study of immune cell communications.

Notifications You must be signed in to change notification settings

PierreBSC/Lymph_node_project

Repository files navigation

Lymph Node project

List of all R codes used for the analysis of single cell data in the paper Blecher et al. on the study of immune cell communications.

Data have not been uploaded yet to GEO but they will be soon.

Analysis scripts

Each 'analysis' script corresponds to a specific part of the paper :

  • Script_total_cells_analysis.R : used to perform the analysis of the total cell fraction. Corresponds to Figure 1 and 3.
  • Script_Antigen_pos_analysis.R : used to perform the analysis of the antigen positive cell fraction. Corresponds to Figure 2.
  • Script_all_mix_cells_analysis.R : used to perform the analysis of the merged total cell and antigen positive fractions. Corresponds to Figure 2 and 3.
  • Script_IFN_NK_depletion.R : used to perform the analysis of the NK/IFNg depletion experiment. Corresponds to Figure 4.

Supplementary analysis scripts

'Supplementary analysis' scripts corresponds to analysis not shown in the main figures of the paper or analysis asked by the reviewers :

  • Supplementary_analysis_total_cells.R : additional QC for total cell fraction.
  • Supplementary_analysis_ag_pos_cells.R : additional QC for antigen positive cell fraction.
  • Supplementary_analysis_all_mix_cells.R : detailed study of migratory dendritic cells diversity.

Other scripts

Other scripts were used to preprocess the Index Sorting Data :

  • AFA_pipeline_script.R : script containing several functions based on FlowCore package to extract, clean and map index sorting data.
  • Index_sorting_total_cells.R : pre-processing of Index Sorting data for total cell fraction.
  • Index_sorting_Antigen_pos.R : pre-processing of Index Sorting data for antigen positive cell fraction.

About

List of all R codes used for the analysis of single cell data in the paper Blecher et al. on the study of immune cell communications.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages