StabMap2021

Scripts used to analyse and generate figure panels for 'StabMap:

Stabilised mosaic single cell data integration using unshared features'.

The StabMap R package can be found here.

Scripts

The scripts folder contains an initialisation script initialise.R and functions for analysis and visualisation.

Analysis

The example folder contains Rmarkdown documents used to analyse and generate figure panels:

• PBMC Multiome example and comparison:
  • PBMC_Multiome_example.Rmd
• Mouse Gastrulation scRNA-seq:
  • MGD_chimera_generate.Rmd
  • MGD_StabMap_example.Rmd
  • MGD_Multihop_example.Rmd
• PBMC Multiome non-overlapping example:
  • PBMC_Multiome_nonoverlapping_example.Rmd
• PBMC CyTOF, ECCITE-Seq and Multiome example:
  • PBMC_CYTOF_generate.Rmd
  • PBMC_ECCITE_generate.Rmd
  • PBMC_Multihop_example.Rmd
• Breast cancer IMC, CITE-Seq and Xenium example:
  • BreastCancer_IMC_generate.Rmd
  • BreastCancer_CITE_generate.Rmd
  • BreastCancer_Xenium_generate.Rmd
  • BreastCancer_Multihop_example.Rmd
• Mouse Gastrulation chimera and seqFISH analysis:
  • MGD_seqFISH_generate.Rmd
  • MGD_chimera_StabMap_SeqFISH_example.Rmd
  • MGD_chimera_StabMap_SeqFISH_example_downstream.Rmd
• Misc:
  • StabMap_workflow_figures.R
  • UINMF_vignette_comparison.Rmd
  • MultiMAP_vignette_comparison.Rmd

These documents assume the existence of folders outside of the scripts working directory, ../Figures/raw/ for graph outputs and ../output/ for analysis output files.

Contact

shila.ghazanfar <at> cruk.cam.ac.uk, shila.ghazanfar <at> sydney.edu.au, or marioni <at> ebi.ac.uk