HST GENOMICS
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Sample deliverables

Transcriptomics, single-cell and genome variants

Bulk RNA-seq differential expression

Bulk RNA-seq differential expression

Public data GEO GSE147507 · human bronchial epithelial cells, SARS-CoV-2 vs mock, n = 3 each

QC, PCA, sample correlation, DESeq2 differential expression, volcano and heatmap, Hallmark enrichment, plus a methods paragraph.

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Single-cell RNA-seq: clustering and annotation

Single-cell RNA-seq: clustering and annotation

Public data 10x Genomics PBMC 10k v3 · human peripheral blood mononuclear cells

QC thresholds with reasons, clustering, marker genes, cell-type annotation and proportions, with annotated result tables.

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Bacterial genome resequencing: variant calling

Bacterial genome resequencing: variant calling

Public data SRA SRR2584866 · E. coli REL606 long-term evolution experiment clone

Read QC, alignment, coverage, SNP/InDel calling and filtering, functional annotation, with the full re-runnable pipeline.

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“Download all files” is a zip archive with the report (HTML and PDF), all figures, result tables and analysis code.

How the examples were made

Public data, real runs, reproducible

  • Data: all from public sources (GEO, 10x Genomics public datasets, NCBI SRA); accession numbers are on the first page of each report.
  • Computation: every number and figure in each report is produced by the attached code; software versions are listed in the methods.
  • Structure: real projects use the same structure (report, figures, tables, code, methods text); content follows the written plan.
  • Privacy: no client data is used.

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