HST GENOMICS
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When custom analysis is needed

Four common situations

Scenario 1

Designs beyond a simple two-group comparison

Time courses, multi-factor designs, paired samples, batches crossed with groups: running the default two-group pipeline can give conclusions that may not hold.

You provide

  • Sample sheet with groups, time points, batches and pairing
  • Raw data or count matrix

What we do

  • We check whether the design supports the comparisons, then choose the model (likelihood-ratio test, mixed model, batch covariates)
  • Model and contrasts written into the plan before work starts

You receive

  • Design-aware differential results and trend clusters
  • A methods paragraph explaining the model choice
Scenario 2

The standard analysis is done, but your question is still open

You have DE lists and a UMAP, but what you need is one cell subset, one pathway or one treatment effect.

You provide

  • Existing results or raw data
  • The cell types, genes or pathways you care about

What we do

  • Targeted follow-up: sub-clustering, trajectories, cell–cell communication, gene-set scoring, TF activity
  • For each analysis we state what it can and cannot support

You receive

  • Figure panels and tables that answer the specific question
  • Draft figure legends and result text
Scenario 3

Reviewers asked for more analyses

A reviewer wants a different method, additional statistics, a validation cohort or extra figures, and the deadline is close.

You provide

  • The reviewer comments
  • Original data and results, code if available

What we do

  • We go through each comment, mark which can be answered by analysis and how long each takes
  • Work is prioritised against your deadline

You receive

  • Additional figures and statistics
  • Text you can adapt for the response letter
Scenario 4

Several data sources need to be combined

Your own data plus public cohorts, transcriptome plus proteome or metabolome, or data from different platforms and batches.

You provide

  • Each data set and how samples correspond
  • Public accession numbers such as GEO or TCGA

What we do

  • We first assess whether the data can be combined and how strong batch effects are, then choose the integration method
  • When public data is used for validation, the approach and its limits are stated

You receive

  • Integrated results and cross-omics association figures
  • A record of data sources and processing
The written plan

What the plan contains

Sent within one working day. Work starts only after you approve it, and delivery is checked against it item by item.

Research question
One or two sentences on what the analysis must answer.
Data and design check
Sample numbers, groups, batches, pairing; whether each comparison is supported, and why not if it is not.
Steps and parameters
Method for each step, key thresholds and the reason for each choice.
Deliverables
Report, each figure, each table, code and methods text, listed item by item.
Timeline
A range in working days, counted from data receipt and plan approval.
Price and revisions
A project price; what is included for questions and revisions after delivery.
Example plans

Three example plans

Example plan A

Mouse liver bulk RNA-seq time course

4 time points × 3 replicates; which genes change over time after treatment, and in what patterns.

  • QC, alignment and quantification; sample correlation and PCA to rule out outliers
  • Likelihood-ratio test for time-dependent genes instead of pairwise tests
  • Trend clustering by expression pattern, enrichment per cluster
  • Time-course plots for genes of interest

Typically 7–10 working days

Example plan B

Tumour single-cell data with public-cohort validation

Six tumour single-cell samples; interest in T-cell subsets before and after treatment, with validation in a public cohort.

  • Integration with batch assessment, annotation to major cell types
  • T-cell sub-clustering, subset markers, proportion and expression changes with treatment
  • Scoring the subset signature in a public cohort such as TCGA, with survival analysis
  • Limitations of public-data validation stated explicitly

Typically 15–20 working days

Example plan C

Analyses for a manuscript revision

Reviewer asks to redo differential analysis with batch correction, add GSEA and ROC curves for a diagnostic model; reply due in three weeks.

  • Each of the three comments assessed against the data
  • Differential analysis redone with batch as covariate, changes compared with the original
  • GSEA and ROC with confidence intervals and cross-validation
  • Text you can adapt for the response letter

Typically 3–7 working days

These examples illustrate how plans are written; they are not client projects. Actual timeline and price are set in the written plan.

Inputs, process, outputs

The whole engagement in one table

StageDetails
DataFASTQ, BAM, count matrices, Seurat/h5ad, Cell Ranger/Space Ranger output, MS quantification tables, public accessions
ContextSample sheet, the question, genes or pathways of interest, target journal, deadline
ProcessWritten plan → your approval → analysis → item-by-item senior review → delivery
DeliveryReport, publication figures (PDF/SVG/PNG), tables (Excel/CSV), re-runnable code and parameters, methods text
After deliveryQuestions answered; revision analyses as agreed in the plan
FAQ

About custom analysis

How much more does custom analysis cost?
It depends on what is added. The plan lists the standard and custom parts separately so you can choose.
I am not sure which analyses I need. Can we talk first?
Yes. Send the data type, design and question; the plan will propose a set of analyses and explain why.
Can you continue from another provider's analysis?
Yes. With raw data or intermediate results we first check the existing results, then build on them.
Will the analysis be tuned to give the result I want?
No. Comparisons the design cannot support are stated in the plan; non-significant results are reported as they are, with possible reasons.
Do you work with clients outside China?
Yes for data analysis: data is transferred online and results are delivered online.

Send us your question and data

You will receive a written plan and quote within one working day.

Request a planSample reports