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Merge pull request #500 from genestack/feature/ODM-12846-gene-summary-analytics
ODM-12846: gene summary analytics
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‎openapi/v1/integrationCurator.yaml‎

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security:
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- Access-token: [ ]
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- Genestack-API-Token: [ ]
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/api/v1/as-curator/omics/cells/analytics/gene-summary:
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post:
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operationId: geneSummaryAsCurator
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summary: "[BETA] Compute and retrieve descriptive statistics and visual summaries for single-cell data."
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tags:
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- "[BETA] Analytics omics queries as Curator"
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description: |+
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This endpoint provides descriptive statistical metrics for gene expression across single-cell datasets.
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It aggregates and summarizes expression data for each gene to help assess variability, distribution,
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and intensity of expression within the population of cells.
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The computed metrics include:
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- `Gene name` - gene identifier.
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- `Cell count` - number of cells with measurable expression for each gene.
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- `Mean expression value`
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- `Median expression value`
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- `Quantiles` - configurable expression percentiles.
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- `Histogram (density)` - binned distribution of expression levels for visualization.
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- `Standard deviation` - dispersion of expression values.
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- `Minimum and maximum values` - range of expression across cells.
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Results are sorted by gene name.
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requestBody:
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required: true
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/GSRequest"
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responses:
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"200":
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description: Gene summary result
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/GSResponse"
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"400":
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content: { }
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description: Invalid data in the request. See the error message for details.
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"401":
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content: { }
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description: |+
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User is not authenticated. Please supply a valid Access Token in the `Authorization`
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HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token`
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header (this token may be obtained from the Genestack UI _Profile_ page).
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"500":
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content: { }
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description: |+
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An internal server error occurred. This indicates an unexpected
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failure in the Genestack system, please file a bug report to support@genestack.com,
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including the error details."
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security:
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- Access-token: [ ]
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- Genestack-API-Token: [ ]
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/api/v1/as-curator/integration/studies/{id}/tasks/publish-versions:
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post:
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description: This endpoint publishes information from staging and creates new
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$ref: "./schemas/cell/DERequest.yaml"
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DEResponse:
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$ref: "./schemas/cell/DEResponse.yaml"
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GSRequest:
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$ref: "./schemas/cell/GSRequest.yaml"
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GSResponse:
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$ref: "./schemas/cell/GSResponse.yaml"
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securitySchemes:
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Access-token:
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in: header

‎openapi/v1/integrationUser.yaml‎

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security:
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- Access-token: [ ]
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- Genestack-API-Token: [ ]
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/api/v1/as-user/omics/cells/analytics/gene-summary:
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post:
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operationId: geneSummaryAsUser
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summary: "[BETA] Compute and retrieve descriptive statistics and visual summaries for single-cell data."
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tags:
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- "[BETA] Analytics omics queries as User"
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description: |+
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This endpoint provides descriptive statistical metrics for gene expression across single-cell datasets.
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It aggregates and summarizes expression data for each gene to help assess variability, distribution,
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and intensity of expression within the population of cells.
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The computed metrics include:
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- `Gene name` - gene identifier.
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- `Cell count` - number of cells with measurable expression for each gene.
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- `Mean expression value`
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- `Median expression value`
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- `Quantiles` - configurable expression percentiles.
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- `Histogram (density)` - binned distribution of expression levels for visualization.
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- `Standard deviation` - dispersion of expression values.
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- `Minimum and maximum values` - range of expression across cells.
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Results are sorted by gene name.
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requestBody:
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required: true
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/GSRequest"
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responses:
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"200":
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description: Gene summary result
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/GSResponse"
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"400":
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content: { }
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description: Invalid data in the request. See the error message for details.
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"401":
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content: { }
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description: |+
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User is not authenticated. Please supply a valid Access Token in the `Authorization`
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HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token`
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header (this token may be obtained from the Genestack UI _Profile_ page).
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"500":
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content: { }
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description: |+
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An internal server error occurred. This indicates an unexpected
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failure in the Genestack system, please file a bug report to support@genestack.com,
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including the error details."
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security:
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- Access-token: [ ]
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- Genestack-API-Token: [ ]
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/api/v1/as-user/integration/link/files/by/study/{id}:
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get:
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operationId: getFilesByStudyAsUser
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$ref: "./schemas/cell/DERequest.yaml"
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DEResponse:
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$ref: "./schemas/cell/DEResponse.yaml"
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GSRequest:
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$ref: "./schemas/cell/GSRequest.yaml"
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GSResponse:
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$ref: "./schemas/cell/GSResponse.yaml"
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securitySchemes:
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Access-token:
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in: header

‎openapi/v1/schemas/cell/GSRequest.yaml‎

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type: object
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properties:
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cellGroup:
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$ref: '#/components/schemas/CellGroupRequest'
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geneNames:
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type: array
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items:
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type: string
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example:
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- "ENSG00000230368"
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- "ENSG00000188976"
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- "ENSG00000188982"
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exQuery:
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type: string
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example: '-3 < value < 3'
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required:
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- geneNames
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components:
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schemas:
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CellGroupRequest:
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type: object
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properties:
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studyFilter:
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type: string
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example: '"Study Source"=ArrayExpress'
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studyQuery:
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type: string
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example: 'RNA-Seq of human dendritic cells'
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sampleFilter:
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type: string
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example: '"Species or strain"="Homo sapiens"'
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sampleQuery:
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type: string
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example: 'Clozapine'
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libraryFilter:
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type: string
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example: '"Library Type"=RNA-Seq-1'
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libraryQuery:
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type: string
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example: 'illumina HiSeq500'
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preparationFilter:
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type: string
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example: 'Digestion=Trypsin'
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preparationQuery:
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type: string
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example: 'reversed-phase liquid chromatography'
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cellQuery:
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type: string
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example: 'cellType=Macrophage,Monocyte'
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searchSpecificTerms:
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type: boolean
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example: false

‎openapi/v1/schemas/cell/GSResponse.yaml‎

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type: object
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properties:
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resultsPerGene:
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type: array
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items:
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$ref: '#/components/schemas/GeneSummaryEntry'
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components:
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schemas:
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GeneSummaryEntry:
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type: object
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description: Per-gene summary statistics.
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properties:
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geneId:
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type: string
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description: Gene identifier.
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example: "ENSG00000111640"
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cellCount:
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type: integer
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format: int32
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description: Number of cells expressing the gene.
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example: 8968167
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mean:
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type: number
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format: double
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description: Mean expression
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example: 7.747614311820911
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median:
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type: number
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format: double
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description: Median expression
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example: 7
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stdDev:
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type: number
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format: double
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description: Standard deviation
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example: 6.499314669429827
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min:
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type: number
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format: double
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description: Minimum value
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example: 1
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max:
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type: number
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format: double
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description: Maximum value
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example: 496
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quantiles:
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type: array
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description: |
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List of quantile values from 0 to 1 (inclusive), with step 0.1
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example: |
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[1, 1, 2, 3, 5, 7, 10, 12, 15, 27, 192]
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items:
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type: number
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format: double
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histogram:
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type: array
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description: |
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Histogram as a list of [binStart, binEnd, count] triples.
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Length depends of the selected sample size, maximum is 20.
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example: |
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[(1, 15.50289002318, 7686678.375), (15.50289002318, 35.49570418233824, 1229164),
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(35.49570418233824, 56.93121325335453, 36531.25), (56.93121325335453, 77.21467372919479, 6910.625)]
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items:
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type: array
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items:
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type: number
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format: double

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