Common questions

Pricing is project-based by default. After you describe your data and goals, you receive a written scope with a fixed-fee quote - no surprise billing from scope creep or pipeline reruns.

For ongoing advisory work, a monthly retainer model is available (typically 8–20 hrs/month). Hourly rates are available for well-defined short tasks (<10 hours). All quotes include:

• Scope of deliverables and file formats
• Estimated timeline with milestones
• Cloud compute cost estimate (billed at cost, not marked up)
• Revision rounds included before final handoff

Invoicing is done via milestone payments - 50% at project kick-off, 50% on delivery. Academic labs and non-profits are welcome to inquire about adjusted rates.

Project duration depends on data volume, pipeline complexity, and iteration needs. Below is a CIGAR-style breakdown of a representative RNA-Seq project (end-to-end):

Rush delivery is available for time-sensitive grant deadlines. All timelines begin after data transfer is confirmed and a kick-off call is scheduled.

Priyansh Pathak - the founder - writes every line of code, runs every pipeline, and interprets every result. OmicsEdge does not employ junior analysts or outsource work offshore.

This means:

• The PhD-level scientist who scoped your project is the same person running the alignment.
• No context switching between account managers and analysts.
• Faster feedback loops, fewer miscommunications, higher code quality.
• You have direct Slack/email access to the person doing the work - not a ticketing system.

OmicsEdge operates as a focused single-expert consultancy with intentionally limited client slots (2–3 active projects at a time). This is by design - capacity is never oversold.

Data security is taken seriously at every layer of the stack:

• Transfer: Data arrives via encrypted S3 presigned URLs or SFTP. No email attachments. No consumer cloud drives.
• Storage: Client buckets are isolated by IAM policy. Server-side encryption (AES-256) at rest. Versioning enabled.
• Compute: Pipelines run in ephemeral cloud environments (AWS Batch / GCP Life Sciences). No data touches unmanaged local storage.
• Deletion: Raw data is deleted from cloud storage 30 days after project close (configurable), unless archival is requested.
• HIPAA: A Business Associate Agreement (BAA) is available for projects involving Protected Health Information (PHI). AWS HIPAA-eligible service set used throughout.

For de-identified research genomics data, HIPAA BAA is optional. For clinical samples retaining patient identifiers, a BAA is required before data transfer begins.

Upon final payment, you own all project-specific code and outputs outright. This includes:

• All Snakemake/Nextflow workflow files
• R/Python analysis scripts
• Conda environments and Docker container configs
• Data outputs, intermediate files, and final figures
• The GitHub repository (transferred to your organization's GitHub)

OmicsEdge retains the right to use anonymized methodology (pipeline architecture patterns, algorithmic approaches) in future client work, but never client data, specific results, or identifying details without explicit written consent. Every engagement is covered by a signed NDA on request.

Both are accepted - the choice affects accuracy and cost:

• POD5 / FAST5 (raw signal): Re-basecalling with the latest Dorado model is performed, giving you the best possible accuracy (Q20+ for R10.4.1 chemistry). Recommended for methylation calling, where signal-level accuracy matters. Adds ~1–2 days to timeline and modest GPU compute cost.
• Pre-basecalled FASTQ: If you've already run Dorado or Guppy, FASTQ is fine for most RNA-Seq, differential expression, and genomic variant applications. Send a NanoStat summary so basecall quality can be assessed upfront.

For short-read Illumina data, FASTQ.gz (gzipped) is the standard input. Raw BCL files from the sequencer are also accepted - demultiplexing is performed at no extra charge.

Yes - this is a significant fraction of the work done at OmicsEdge. Specific support offered:

• Grant figures: Publication-quality vector figures (PDF/SVG) generated in R (ggplot2) or Python (seaborn/matplotlib), formatted to journal or NIH submission specs.
• Methods text: Draft bioinformatics methods sections - tool versions, parameter choices, statistical thresholds, and reproducibility statements - ready to paste into your manuscript.
• Preliminary data: Full analysis from raw data to results for R01 / R21 / NSF preliminary data sections. Turnaround optimized for grant deadlines.
• Peer review responses: Reanalysis or additional analyses requested by reviewers ("please show X with method Y").

Authorship expectations are discussed upfront based on the nature and scope of the analytical contribution. For primarily service-based analysis, authorship is not required but appreciated in the Acknowledgements.

Getting started is a three-step process:

1. Submit an inquiry via the contact form. Describe your data (organism, assay, approximate sample count) and your primary biological question. No commitment required.
2. Feasibility assessment (48h): A written reply within 48 hours confirming whether the work is in scope, what a realistic timeline looks like, and a ballpark cost range.
3. Kick-off call + scope doc: A 45-minute call to align on goals, review data quality, and confirm deliverables. You receive a signed scope document before any work begins.