Deliverables - OmicsEdge Consulting

git.diff · before=raw_data · after=project_close · files_changed=∞

Before → After

The transformation from raw sequencing files to a complete, publication-ready deliverable package.

$ git diff HEAD~1 HEAD -- project/ --stat 6 files changed · 2,847 insertions(+) · 12 deletions(−)

@@ -0,0 +1 @@ RAW INPUT STATE → OMICSEDGE DELIVERY STATE
− data/raw/sample_001.fastq.gz  [unprocessed · Q14 avg · no QC]
− notes/lab_notebook_scan.pdf  [undocumented methods]
− analysis/attempt_v3_FINAL_2.R  [non-reproducible · hardcoded paths]
− figures/volcano_plot_low_res.png  [300dpi · non-vector · wrong palette]
− results/DEG_list.xlsx  [no FDR cutoff documented]
− # no pathway analysis performed
− # no statistical validation report
− # no cloud infrastructure · runs on local 16-core only
+ pipeline/Snakefile  [versioned · Docker-locked · Snakemake 8.x]
+ pipeline/envs/rnaseq.yaml  [Conda env · pinned deps · reproducible]
+ pipeline/config.yaml  [all params documented · defaults explained]
+ qc/multiqc_report.html  [FastQC · NanoPlot · pass/fail summary]
+ results/deseq2_results.tsv  [padj · log2FC · baseMean · full table]
+ results/fgsea_hallmarks.tsv  [pathway NES · pval · leading edge genes]
+ figures/volcano_plot.pdf  [vector · 300dpi · journal palette · labeled]
+ figures/heatmap_top50.pdf  [hierarchical clustering · z-scored]
+ figures/pathway_dotplot.pdf  [top 20 hallmarks · NES-colored]
+ report/interpretation_report.pdf  [written · annotated · method detail]
+ infra/terraform/main.tf  [AWS Batch · IAM · S3 · reproducible compute]
+ README.md  [step-by-step · how to reproduce · contact info]

          +2,847 insertions
          −12 deletions
          net change: reproducible + publishable
        

deliverables.index · n=6 · included=all_engagements

Six standard deliverables

Included in every engagement unless otherwise scoped. Extensions available for specialty outputs (GEO submission prep, Zenodo archival, Docker Hub push).

Versioned Pipeline Repository

A fully annotated GitHub repository transferred to your organization. Snakemake or Nextflow workflow, pinned Conda environments, Dockerfile, config files with documented parameters, and a step-by-step README. Any lab member can re-run the analysis from scratch.

GitHub repo Snakemake/Nextflow Docker Conda envs

QC Report (MultiQC)

A comprehensive MultiQC HTML report covering per-sample quality metrics: adapter content, base quality distributions, duplication rates, mapping rates, insert sizes, and PHRED score profiles. Every sample is flagged pass/warn/fail with decision rationale documented.

multiqc_report.html FastQC NanoPlot per-sample TSV

Analysis Results Tables

Full gene-level (or peak-level) result tables in machine-readable TSV format: all genes tested, log2FC, baseMean, Wald statistic, p-value, padj. Separate tables for each contrast, with FDR cutoff justification documented. GSEA/pathway enrichment tables with NES, pval, padj, leading edge.

DESeq2 results.tsv fgsea.tsv peak_calls.bed counts_matrix.tsv

Publication-Ready Figures

Vector PDF and PNG figures generated in R (ggplot2) or Python (matplotlib/seaborn). Volcano plots, MA plots, GSEA enrichment plots, heatmaps, genome browser tracks, and assay-specific visualizations. Color palettes matched to journal style guides (PNAS, Nature, Cell family). All fonts embedded.

PDF (vector) PNG 600dpi ggplot2/mpl source panel-ready

Written Interpretation Report

A written PDF report (typically 8–20 pages) covering: methods description (ready to paste into manuscript), per-figure biological interpretation, caveats and assumptions, suggested follow-up experiments, and a bibliography with tool citations and version numbers. Written for a biologist audience, not just a bioinformatics one.

methods_text.docx interpretation_report.pdf citations.bib

Walkthrough Call + Handoff

A 45–60 minute call (recorded on request) walking through every deliverable: how to re-run the pipeline, how to interpret each figure, what the statistical thresholds mean biologically, and what to do next. Includes a 30-day async Q&A window after delivery - questions answered within 48 hours. No black-box handoffs.

Zoom/Meet call recorded session 30-day async QA

turnaround.index · format=assay_class · unit=business_days

Turnaround times

From receipt of complete data transfer to first delivery. Timelines assume <30 samples and no iterative redesign mid-project.

Assay / Service Type	Samples	Standard	Rush	Includes
Bulk RNA-Seq (DESeq2 + GSEA)	4–24	10–14 days	5–7 days	QC · alignment · DE · pathways · figures · report
Ribo-Seq (translational efficiency)	4–12	14–18 days	8–10 days	riboriboQC · ORF detection · TE analysis · codon analysis
TERA-Seq / 5′-end capping analysis	4–8	14–21 days	10–14 days	5′ adapter trimming · CAP-score · TSS calling · DE
m6A-Seq / METTL3-IP analysis	4–16	14–18 days	8–12 days	m6Aviewer · exomePeak2 · MEME motif · gene-level annotation
scRNA-Seq (Seurat / 10x Chromium)	1–8 runs	18–28 days	12–18 days	cell ranger · QC · clustering · cell typing · trajectory
Oxford Nanopore - RNA / cDNA	2–12	10–16 days	7–10 days	Dorado basecall · minimap2 · bambu isoforms · DE
Multi-omics integration (MOFA2)	varies	21–35 days	case-by-case	MOFA2 LF · variance partition · cross-omics correlation
Cloud infra migration (HPC → AWS)	N/A	21–42 days	case-by-case	Terraform · IAM · S3 · Batch · cost model · docs

* Rush delivery adds a 20% surcharge. All timelines begin after data transfer confirmation and kick-off call. Timelines are estimates; actual delivery may vary based on data quality and project complexity. Scope document specifies binding delivery dates.

What you receive

Before → After

Six standard deliverables

Turnaround times

Ready to see this in your hands?