IBL/cBio

All you need is

<script src="https://ibl.github.io/cbio/cbio.js"></script>

Live at: https://ibl.github.io/cbio/

---

Experimenting with the possibility of having cBioPortal Web API as a client side JavaScript library. Since the API is not CORS enabled, a Google Script was implemented as a middle layer. The basic idea is to mimic the query syntax with objects constructed as

cbio.\( callbackFunction , { argument_i : value_i , ... } );

Many thanks to MSKCC's cBioPortal team - this is a great public service !

---

get

cbio.get = function(cmd,fun,parms)

All commands below are a type of bio.get, sy submitting command cmd to cbio WebAPI and process it through callback function fun with option parameters parms. For example

cbio.getTypesOfCancer is cbio.get('getTypesOfCancer')

and

cbio.getProteinArrayData(
	{
		case_set_id:"coadread_tcga_RPPA",
		array_info:1
	},
	function(x){console.log(cbio.table(x))}
)

is the same as

cbio.get(
	"getProteinArrayData",
	{
		case_set_id:"coadread_tcga_RPPA",
		array_info:1
	},
	function(x){console.log(cbio.table(x))}
)

or

cbio.get(
	"getProteinArrayData",
	function(x){console.log(cbio.table(x))},
	{
		case_set_id:"coadread_tcga_RPPA",
		array_info:1
	}
)

(note the code will check for switch over vars fun and parms)

getTypesOfCancer

cbio.getTypesOfCancer( callbackFunction );

example:

	
cbio.getTypesOfCancer()

getCancerStudies

cbio.getCancerStudies( callbackFunction );

example:

	
cbio.getCancerStudies()

getGeneticProfiles

cbio.getGeneticProfiles( "cancer study ID (required)" , callbackFunction)

example:

	cbio.getGeneticProfiles("gbm_tcga") 

getCaseLists

cbio.getCaseLists(cancer_study_id)

example:

cbio.getCaseLists("gbm_tcga") 

getProfileData

cbio.getProfileData({ 
	case_set_id: "case set ID (required)" , 
	genetic_profile_id: "one or more genetic profile IDs (required)",
	gene_list: "one or more HUGO Gene Symbols or Entrez Gene IDs (required)" 
})

examples:

cbio.getProfileData({
	case_set_id:"gbm_tcga_all",
	genetic_profile_id:"gbm_tcga_mutations",
	gene_list:["BRCA1","BRCA2","TP53"]
})

cbio.getProfileData({
	case_set_id:"gbm_tcga_all",
	genetic_profile_id:["gbm_tcga_log2CNA","gbm_tcga_gistic"],
	gene_list:"EGFR"
})

getMutationData

cbio.getMutationData({ 
	genetic_profile_id: "one or more mutation profile IDs (required)",
	case_set_id: "case set ID (optional)",
	gene_list: "one or more HUGO Gene Symbols or Entrez Gene IDs (required)"
})

examples:

cbio.getMutationData({
	case_set_id:"gbm_tcga_all",
	genetic_profile_id:"gbm_tcga_mutations",
	gene_list:["EGFR","PTEN"]
})

cbio.getMutationData({
	genetic_profile_id:["ov_tcga_mutations","ucec_tcga_mutations"],
	gene_list:"BRCA1"
})

getClinicalData

cbio.getClinicalData("case set ID (required)")

example:

	
	cbio.getClinicalData("ov_tcga_all") 

getProteinArrayInfo

cbio.getProteinArrayInfo({
	cancer_study_id: "cancer study ID (required)",
	protein_array_type:"protein_level or phosphorylation",
	 gene_list:["one or more HUGO Gene Symbols or Entrez Gene IDs"]
})

examples:

cbio.getProteinArrayInfo({cancer_study_id:"coadread_tcga"})

cbio.getProteinArrayInfo({
	cancer_study_id:"coadread_tcga",
	protein_array_type:"phosphorylation"
})

cbio.getProteinArrayInfo({
	cancer_study_id:"coadread_tcga",
	protein_array_type:"protein_level",
	gene_list:["ERBB2","TP53"]
})

getProteinArrayData

cbio.getProteinArrayData({
	case_set_id: "case set ID (required)",
	array_info: “[1 or 0]. If 1, antibody information will also be exported”
})

examples:

	cbio.getProteinArrayData("coadread_tcga_RPPA")

	cbio.getProteinArrayData({case_set_id:"coadread_tcga_RPPA"})

	cbio.getProteinArrayData({case_set_id:"coadread_tcga_RPPA",array_info:1})

---

getLinkStudy

cbio.getLinkStudy(parms)

example:

	cbio.getLinkStudy({cancer_study_id:"gbm_tcga",gene_list:["EGFR","NF1"]}) // returns URL

	cbio.getLinkStudy({cancer_study_id:"gbm_tcga",gene_list:["EGFR","NF1"]})  // opens URL

getLinkCase

cbio.getLinkCase(parms)

examples:

	cbio.getLinkCase({case_id:"TCGA-81-5910",cancer_study_id:"gbm_tcga"})  // returns URL

	cbio.getLinkCase({case_id:"TCGA-81-5910",cancer_study_id:"gbm_tcga"},'cbio')  // opens URL

oncoprint

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