Six perspectives on immune biology.
Focused downstream analyses shaped by your biological question, study design and available data.
01 / FOR RESEARCH USE
Immune Repertoire
Question: How are TCR/BCR clonotypes composed, diverse, expanded and shared?
Inputs: Annotated repertoire tables and sample metadata.
Typical outputs: QC summaries, diversity comparisons and clonotype visualizations.
02 / FOR RESEARCH USE
Immunogenicity & Neoantigens
Question: Which candidate antigens merit prioritisation in genomic and immune context?
Inputs: Somatic variants, HLA typing and expression where available.
Typical outputs: Annotated candidate tables and transparent prioritisation criteria. Computational predictions require experimental validation.
03 / FOR RESEARCH USE
Transcriptomics
Question: Which expression patterns, contrasts and pathways are evident in the study?
Inputs: Count matrices and experimental metadata.
Typical outputs: QC, contrast tables and pathway summaries.
04 / FOR RESEARCH USE
Tumor Immune Microenvironment
Question: How do immune and stromal composition estimates relate to immune signatures?
Inputs: Bulk expression and relevant annotations.
Typical outputs: Deconvolution estimates, signature scores and cohort comparisons. These are method-dependent estimates.
05 / FOR RESEARCH USE
Single-cell Immunology
Question: Which immune cell states and heterogeneity are represented?
Inputs: Single-cell count matrices, metadata and optional paired V(D)J.
Typical outputs: QC, embeddings, cell annotations and state comparisons.
06 / FOR RESEARCH USE
Cancer Genomics
Question: What somatic variation and genomic context should be compared?
Inputs: Annotated variants, copy-number profiles and cohort metadata where available.
Typical outputs: Variant summaries, oncoplots and integrative comparisons.
Scope, deliverables and limitations are agreed for each research project.
Bring a focused research question.
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