{
 "schema": "aiblocks-page/1",
 "id": "prepare-bulk-rna-results-with-explicit-contrasts",
 "type": "workflow",
 "name": "Turn bulk RNA counts into checked results",
 "summary": "Attach counts and sample metadata. Get an explicit comparison, analysis records and figures with unresolved quality issues.",
 "headline": "Turn bulk RNA counts into checked results",
 "subhead": "Attach counts and sample metadata. Get an explicit comparison, analysis records and figures with unresolved quality issues.",
 "job": {
  "id": "research-topics",
  "name": "Research a topic properly"
 },
 "level": "advanced",
 "thinking": "high",
 "tested": true,
 "updated": "2026-11-03",
 "first_published": "2026-10-25",
 "inputs": [
  {
   "type": "spreadsheet",
   "required": true,
   "label": "Spreadsheet",
   "what": "a spreadsheet with its data, formulas and charts"
  },
  {
   "type": "dataset",
   "required": true,
   "label": "Dataset",
   "what": "data files to process or analyse, such as a CSV or JSON export, logs, lab or sensor files, with their format and where they came from"
  }
 ],
 "outputs": [
  {
   "type": "spreadsheet",
   "required": true,
   "label": "Spreadsheet",
   "what": "a spreadsheet with its data, formulas and charts"
  },
  {
   "type": "document",
   "required": true,
   "label": "Document",
   "what": "a finished document, such as a Word file, a PDF or a page of notes"
  },
  {
   "type": "audit_report",
   "required": true,
   "label": "Audit report",
   "what": "findings with evidence, severity, missing inputs and next actions"
  }
 ],
 "you_give": [
  "COUNT_SOURCES: attach raw gene counts or supported quantification files, orientation, tool versions and reference provenance.",
  "SAMPLE_METADATA: attach unique sample IDs, biological units, condition, batch and relevant covariates.",
  "COMPARISON: state the explicit contrast, reference levels, design formula, exclusions, prefilter and error-rate threshold.",
  "RUN_SCOPE: identify the permitted local environment, package versions and output folder."
 ],
 "you_get": [
  "Validated count/metadata handoff and analysis code",
  "Full result tables, diagnostics, figures and interpretation limits"
 ],
 "use_when": [
  "Preparing a bulk RNA-seq comparison for research review"
 ],
 "skip_when": [
  "Your data is single-cell RNA: use the Single-cell RNA count analyst.",
  "You only need the counts table built from reads or Salmon output: use the RNA-seq comparison preparer.",
  "You already have a results table and only need a chart: use the Journal-ready figure maker."
 ],
 "output_sample": {
  "input": [
   "Raw gene counts, or quantification files, with tool versions and reference build",
   "A sample sheet with sample IDs, condition, batch and other covariates",
   "The comparison you want, with reference levels, design and error-rate threshold",
   "The local environment and output folder you may use"
  ],
  "prerequisites": [
   "An AI that can run code on your files"
  ],
  "output": [
   {
    "name": "Validated counts and metadata",
    "contains": "A genes-by-samples counts table, sample sheet, quality checks and a list of exclusions."
   },
   {
    "name": "Design and contrast record",
    "contains": "The design formula, reference levels and the exact comparison that was tested."
   },
   {
    "name": "Result tables and diagnostics",
    "contains": "Full tables with corrected p-values, effect sizes, warnings and missing values kept in."
   },
   {
    "name": "Figures and captions",
    "contains": "Labelled plots with uncertainty, plotting code and the source data behind each one."
   },
   {
    "name": "Version and parameter manifest",
    "contains": "Tool versions, settings, which code ran, and the quality issues still open."
   }
  ]
 },
 "how_to_use": [
  "Download the complete workflow or agent pack and unzip it.",
  "Give the complete folder to your AI. Start with START_HERE.txt, then provide the named inputs in the coordinator skill.",
  "Follow its checkpoints and check the evidence before using any output. Agent packs run one requested cycle; they do not create a schedule."
 ],
 "checks": [
  "Count provenance, sample alignment and biological replication are explicit.",
  "Intended contrast, reference levels and design are recorded.",
  "Tables retain missing values, warnings and filtering choices.",
  "Figures and captions match full result tables."
 ],
 "steps": [
  {
   "position": 1,
   "id": "rna-seq-comparison-preparer",
   "name": "RNA-seq comparison preparer",
   "summary": "Share sequencing output and a sample sheet. Get checked gene counts and matching sample details for comparison.",
   "url": "https://useaiblocks.com/skills/rna-seq-comparison-preparer"
  },
  {
   "position": 2,
   "id": "rna-seq-group-difference-finder",
   "name": "RNA-seq group difference finder",
   "summary": "Share raw gene counts and group details. Get tested gene differences, adjusted p-values, effect sizes and plots, with input checks.",
   "url": "https://useaiblocks.com/skills/rna-seq-group-difference-finder"
  },
  {
   "position": 3,
   "id": "journal-ready-figure-maker",
   "name": "Journal-ready figure maker",
   "summary": "Give it your data. Get clear, honest, colour-safe figures with uncertainty shown, sized for journal export.",
   "url": "https://useaiblocks.com/skills/journal-ready-figure-maker"
  }
 ],
 "next": [
  {
   "name": "Gene list pathway finder",
   "url": "https://useaiblocks.com/skills/gene-list-pathway-finder",
   "why": "Gene list pathway finder"
  }
 ],
 "source": null,
 "credits": [],
 "files": [
  "references/practice-case.md"
 ],
 "links": {
  "page": "https://useaiblocks.com/workflows/prepare-bulk-rna-results-with-explicit-contrasts",
  "markdown": "https://useaiblocks.com/workflows/prepare-bulk-rna-results-with-explicit-contrasts.md",
  "json": "https://useaiblocks.com/workflows/prepare-bulk-rna-results-with-explicit-contrasts.json",
  "instructions": "https://useaiblocks.com/skills/prepare-bulk-rna-results-with-explicit-contrasts/SKILL.md",
  "download": "https://useaiblocks.com/skills/prepare-bulk-rna-results-with-explicit-contrasts.zip",
  "api_item": "https://useaiblocks.com/api/v1/items/prepare-bulk-rna-results-with-explicit-contrasts",
  "api_document": "https://useaiblocks.com/api/v1/documents/workflow/prepare-bulk-rna-results-with-explicit-contrasts",
  "mcp": "https://useaiblocks.com/mcp"
 }
}