{"Id":"86f5028d-1adb-402d-91d1-3cdaf86a4e32","CanonicalId":"","Url":"https://doi.org/10.17632/cydmwsfztj.1","Name":"Scripts for neighborhood analysis","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.","ResourceType":"CodePipelineTechnology","ParentResourceType":"Technology","DefiningManuscriptId":"PMID30713109","Publications":[],"Contributors":[{"Role":{"CanonicalId":"hirn-cv-ResourceRole-producer","Url":"resources.hirnetwork.org/api/v1/CV/","Name":"Producer","OntologyId":"HIRN"},"HirnUserId":"clive_wasserfall@hirnetwork.org","FirstName":"Clive","LastName":"Wasserfall","EmailAddress":"clive@uf.edu","Organization":"University of Florida","Consortia":[]},{"Role":{"CanonicalId":"hirn-cv-ResourceRole-producer","Url":"resources.hirnetwork.org/api/v1/CV/","Name":"Producer","OntologyId":"HIRN"},"HirnUserId":"irina_kusmartseva@hirnetwork.org","FirstName":"Irina","LastName":"Kusmartseva","EmailAddress":"inkusmartseva@ufl.edu","Organization":"University of Florida","Consortia":["HPAC"]},{"Role":{"CanonicalId":"hirn-cv-ResourceRole-producer","Url":"resources.hirnetwork.org/api/v1/CV/","Name":"Producer","OntologyId":"HIRN"},"HirnUserId":"harry_nick@hirnetwork.org","FirstName":"Harry","LastName":"Nick","EmailAddress":"hnick@ufl.edu","Organization":"University of Florida","Consortia":["CBDS"]},{"Role":{"CanonicalId":"hirn-cv-ResourceRole-producer","Url":"resources.hirnetwork.org/api/v1/CV/","Name":"Producer","OntologyId":"HIRN"},"HirnUserId":"fabrizio_thorel@hirnetwork.org","FirstName":"Fabrizio","LastName":"Thorel","EmailAddress":"fabrizio.thorel@unige.ch","Organization":"University of Geneva","Consortia":["CTAR","CBDS"]},{"Role":{"CanonicalId":"hirn-cv-ResourceRole-producer","Url":"resources.hirnetwork.org/api/v1/CV/","Name":"Producer","OntologyId":"HIRN"},"HirnUserId":"pedro_herrera@hirnetwork.org","FirstName":"Pedro","LastName":"Herrera","EmailAddress":"pedro.herrera@unige.ch","Organization":"University of Geneva","Consortia":["CTAR","CBDS"]},{"Role":{"CanonicalId":"hirn-cv-ResourceRole-producer","Url":"resources.hirnetwork.org/api/v1/CV/","Name":"Producer","OntologyId":"HIRN"},"HirnUserId":"mark_atkinson@hirnetwork.org","FirstName":"Mark","LastName":"Atkinson","EmailAddress":"atkinson@pathology.ufl.edu","Organization":"University of Florida","Consortia":["CBDS","HPAC","OPP"]},{"Role":{"CanonicalId":"hirn-cv-ResourceRole-producer","Url":"resources.hirnetwork.org/api/v1/CV/","Name":"Producer","OntologyId":"HIRN"},"HirnUserId":"bernd_bodenmiller@hirnetwork.org","FirstName":"Bernd","LastName":"Bodenmiller","EmailAddress":"bernd.bodenmiller@imls.uzh.ch","Organization":"University of Zurich","Consortia":["CBDS"]}],"Vendor":{"id":null,"Name":null,"Url":null},"VendorResourceName":null,"VendorResourceUrl":null,"VendorCatNumber":null,"VendorLotNumber":null,"DateCreated":"2019-04-26T01:22:19.5718812+00:00","DateModified":"2022-07-01T03:35:15.7183598+00:00","VersionId":"1","ModelVersion":"4.0","TechnologyData":{"Dependencies":[],"AssayTechnologyData":{"BioSampleType":[],"CellsTestedWith":[],"AssayTarget":{"CanonicalId":null,"Url":null,"Name":null,"OntologyId":null},"AssayCategory":{"CanonicalId":null,"Url":null,"Name":null,"OntologyId":null},"TechnologyType":{"CanonicalId":null,"Url":null,"Name":null,"OntologyId":null},"TechnologyPlatform":null,"CompatibleTools":[]},"DeviceEquipmentTechnologyData":{"CompatibleTools":[],"CellsTestedWith":[],"Placeholder":"Test"},"ServiceTechnologyData":{"CellsTestedWith":[],"Placeholder":"test"},"CodePipelineTechnologyData":{"Placeholder":"Test"}}}