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create Quick Start Guide #39

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Tracked by #35
sreichl opened this issue Dec 18, 2024 · 0 comments
Open
Tracked by #35

create Quick Start Guide #39

sreichl opened this issue Dec 18, 2024 · 0 comments
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@sreichl
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sreichl commented Dec 18, 2024

  • a "hello world" toy example to download MrBiomics and run instantly.
  • minimal but real bio data
    • minimal runtime (5-30s)
    • minimal code/config complexity
    • minimal output complexity (1 pretty plot)
  • Biologically meaningful example:
    • dea_limma: Bulk RNA-seq analysis with volcano plot / heatmap as output
    • enrichment_analysis: multiple related gene lists with meaningful clustered bubble plot as output
      • gene lists from RNAseq recipe ie hematopoietic signatures or
      • just take celltype cluster DEA lists from some scRNAseq data
      • either call the mystery sets and choose a database that clearly shows cell types / the answer
      • in case of COPD fgsea example use: REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION
  • This should be at the top of the wiki features "Start here with the Quick Start" or similar
  • Should include everything from installation to plot
@sreichl sreichl self-assigned this Dec 18, 2024
@sreichl sreichl changed the title create Quick Start create Quick Start Guide Dec 18, 2024
@sreichl sreichl mentioned this issue Dec 18, 2024
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