Resource Type
Technology / CodePipelineTechnology
Resource Name

Scripts for neighborhood analysis

Canonical Identifier
Description
R and histoCAT functions for neighborhood analysis. Custom scripts import cell type and pseudotime information into histoCAT. An expansion of 3 pixels was used to detect cell neighbors. The presence of significant cell type association or avoidance was determined using 999 random permutations of cell type labels and a significance threshold of p < 0.01. All other parameters and methods were chosen as suggested defaults.
Contributors
NameOrganizationConsortiumContact
Clive WasserfallUniversity of Florida Contact
Irina KusmartsevaUniversity of FloridaHPAC Contact
Harry NickUniversity of FloridaCBDS Contact
Fabrizio ThorelUniversity of GenevaCTAR, CBDS Contact
Pedro HerreraUniversity of GenevaCTAR, CBDS Contact
Mark AtkinsonUniversity of FloridaCBDS, HPAC, OPP Contact
Bernd BodenmillerUniversity of ZurichCBDS Contact
Defining Manuscript Identifier


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