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  "License": "MIT + file LICENSE",
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    "gexp_qc_prepare_boxplot_data",
    "gexp_qc_prepare_density_data",
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    "gexpipe_batch_covariate_info",
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    "gexpipe_deseq2_design",
    "gexpipe_has_mixed_platforms",
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      "title": "Align RNA-seq count-matrix column names with GEO sample metadata",
      "topics": [
        "gexp_align_rnaseq_sample_names"
      ]
    },
    {
      "page": "gexp_batch_correct",
      "title": "Variance-based gene filtering and batch correction",
      "topics": [
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      ]
    },
    {
      "page": "gexp_download_finalize_common_genes",
      "title": "Finalize common genes and combined matrix after download/mapping",
      "topics": [
        "gexp_download_finalize_common_genes"
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    },
    {
      "page": "gexp_download_normalize_ids_for_overlap",
      "title": "Normalize dataset row IDs to gene symbols for overlap",
      "topics": [
        "gexp_download_normalize_ids_for_overlap"
      ]
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    {
      "page": "gexp_download_one_microarray_gse",
      "title": "Download and parse one microarray GSE",
      "topics": [
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    },
    {
      "page": "gexp_download_one_rnaseq_gse",
      "title": "Download and parse one RNA-seq GSE",
      "topics": [
        "gexp_download_one_rnaseq_gse"
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    },
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      "title": "Fetch sample metadata from GEO series matrix fallback",
      "topics": [
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    },
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      "title": "Build diagnostic log text when no common genes are found",
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      "title": "Normalize microarray and RNA-seq datasets and compute common genes",
      "topics": [
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      "topics": [
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      "page": "gexp_prepare_download_dirs",
      "title": "Prepare clean download directories for current run",
      "topics": [
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      "title": "Map combined-expression sample IDs to source GSE datasets",
      "topics": [
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      "topics": [
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      "page": "gexp_qc_exclude_samples",
      "title": "Exclude selected samples from download/QC state lists",
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      "page": "gexpipe_deseq2_design",
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      "title": "GExPipe: An Integrated Pipeline for Gene Expression Analysis",
      "author": "Safa Rafique, Naeem Mahmood, Muhammad Farooq Sabar",
      "engine": "knitr::rmarkdown",
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        "Vignette outline",
        "How the Shiny app is organised",
        "Installation",
        "From Bioconductor (recommended)",
        "From GitHub (available before Bioconductor release)",
        "Run latest code for analysis",
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        "Step 2 — QC & Visualization",
        "Step 3 — Normalize Data",
        "Step 4 — Select Groups",
        "Step 5 — Batch Correction",
        "Phase 2 — Gene discovery",
        "Step 6 — Differential Expression Analysis",
        "Step 7 — WGCNA Network Analysis",
        "Step 8 — Common Genes (DEG & WGCNA) & Enrichment",
        "Phase 3 — Candidate refinement",
        "Step 9 — PPI Interaction",
        "Step 10 — Machine Learning Process",
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      "created": "2026-03-29 13:48:11",
      "modified": "2026-07-15 13:52:02",
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