{
  "id": "lib-process:bioinformatics--rnaseq-differential-expression",
  "_kind": "LibraryProcess",
  "_file": "generated-library/processes.yaml",
  "_cluster": "generated-library",
  "attributes": {
    "displayName": "rnaseq-differential-expression",
    "description": "RNA-seq Differential Expression Analysis - Comprehensive RNA-seq analysis workflow\nfor identifying differentially expressed genes between experimental conditions. Includes\nnormalization, statistical modeling, and pathway enrichment.",
    "libraryPath": "library/specializations/domains/science/bioinformatics/rnaseq-differential-expression.js",
    "specialization": "bioinformatics",
    "references": [
      "- DESeq2: https://bioconductor.org/packages/DESeq2/\n- edgeR: https://bioconductor.org/packages/edgeR/\n- STAR Aligner: https://github.com/alexdobin/STAR\n- Salmon: https://combine-lab.github.io/salmon/\n- clusterProfiler: https://bioconductor.org/packages/clusterProfiler/"
    ],
    "example": "const result = await orchestrate('specializations/domains/science/bioinformatics/rnaseq-differential-expression', {\n  projectName: 'Drug Treatment Study',\n  samples: [{ id: 'S1', condition: 'treatment' }, { id: 'S2', condition: 'control' }],\n  conditions: { treatment: 'Drug_A', control: 'Vehicle' },\n  referenceGenome: 'GRCh38'\n});",
    "usesAgents": [
      "general-purpose"
    ]
  },
  "outgoingEdges": [
    {
      "from": "lib-process:bioinformatics--rnaseq-differential-expression",
      "to": "skill-area:data-analysis",
      "kind": "lib_requires_skill_area",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--rnaseq-differential-expression",
      "to": "skill-area:statistical-analysis",
      "kind": "lib_requires_skill_area",
      "attributes": {
        "weight": 0.7
      }
    },
    {
      "from": "lib-process:bioinformatics--rnaseq-differential-expression",
      "to": "skill-area:python-data-pipelines",
      "kind": "lib_requires_skill_area",
      "attributes": {
        "weight": 0.5
      }
    },
    {
      "from": "lib-process:bioinformatics--rnaseq-differential-expression",
      "to": "domain:bioinformatics",
      "kind": "lib_applies_to_domain",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--rnaseq-differential-expression",
      "to": "role:research-engineer",
      "kind": "lib_involves_role",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--rnaseq-differential-expression",
      "to": "role:biomedical-engineer",
      "kind": "lib_involves_role",
      "attributes": {
        "weight": 0.7
      }
    },
    {
      "from": "lib-process:bioinformatics--rnaseq-differential-expression",
      "to": "workflow:experiment-design",
      "kind": "lib_implements_workflow",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--rnaseq-differential-expression",
      "to": "specialization:biomedical-informatics",
      "kind": "lib_belongs_to_specialization",
      "attributes": {
        "weight": 1
      }
    },
    {
      "from": "lib-process:bioinformatics--rnaseq-differential-expression",
      "to": "specialization:bioinformatics",
      "kind": "lib_belongs_to_specialization",
      "attributes": {
        "weight": 0.9
      }
    }
  ],
  "incomingEdges": []
}