Notebook Gallery#
Rendered walkthroughs for the key mirpy workflows. All notebooks are included as-is with pre-computed outputs; they are not re-executed during the docs build.
Parsing And Repertoire Basics#
parsing_example — Parse VDJdb, AIRR, and VDJtools files into repertoire objects.
sample_repertoire_overview — Load a multi-locus SRA cohort and inspect coverage statistics.
gene_usage_correction — Batch-correct V/J gene usage across donors and derive PCA/UMAP embeddings.
diversity_analysis — Reproduce diversity tables, rarefaction, coverage, Hill curves, and MS vs healthy cohort comparisons.
Graph And Sequence Analysis#
gene_similarity — Compare germline V gene amino-acid sequences via the GermlineAligner API.
token_graph — Build bipartite k-mer/clonotype graphs and filter by sequence motifs.
edit_distance_graph — Construct Hamming/Levenshtein edit-distance graphs from junction sequences.
vdjdb_junction_graph — Analyse multi-epitope junction Hamming graphs from VDJdb.
metaclonotype_examples — Build, attach, summarize, and analyze metaclonotypes for functional diversity workflows.
metaclonotype_method_compare — Compare ALICE, TCRnet, TCRdist, edit-distance, TCREmp, and GLIPH metaclonotype clustering methods; benchmark paired-chain combined vs native TCREmp; concordance via ARI.
Biomarker Detection#
- ALICE Analysis: YFV19, Ankylosing Spondylitis (AS), and MLR TCR-seq Datasets
- Yellow Fever (YF) Dataset
- Ankylosing Spondylitis (AS) Dataset
- Mixed Lymphocyte Reaction (MLR) Dataset
- T-cell repertoire annotation and motif discovery (TCRNET-style)
- GLIPH-like multi-family enrichment and full-graph clustering (TRB)
- VDJBet YF Analysis (Rmd-aligned)
alice_analysis — ALICE antigen-expanded clone detection on YF, AS, and MLR datasets.
tcrnet_analysis — TCRNET enrichment for CMV+ vs B35+ donors with VDJdb annotation.
gliph_analysis — GLIPH-style multi-family token enrichment and clonotype graph clustering.
vdjbet_yf — VDJBet disease-associated overlap analysis on YFV vaccine time-series samples.
motif_logos — PWM construction, standard IC logos, and background-normalised logos for GILGFVFTL and B27 AS CDR3 motifs.
Sequence Logo Analysis#
Aging And Cohort Overlap#
aging_analysis — Donor-vs-pool overlap trends across aging, using the shared-worker many-vs-pool overlap path for faster repeated scoring.
aging_analysis_functional — Compare clonotypic and functional diversity, rarefaction, and F overlap for the AIRR benchmark aging cohort. Metaclonotypes built via 1-mismatch Hamming edit graph + Louvain clustering.
Pgen And Selection Analysis#
pgen_analysis — Benchmark OLGA exact, Monte-Carlo, and hash-enumeration Pgen strategies; analyse the Q-factor (thymic selection correction) on VDJdb clonotypes.
TCREmp Embeddings#
tcrdist_analysis — Compute TCRdist matrices, score radius-based neighborhoods, and derive metaclonotypes.
tcremp_vdjdb_analysis — Single-chain TCREmp on VDJdb epitope-labelled clonotypes with UMAP projection.
tcremp_vdjdb_analysis_paired — Paired TRA/TRB TCREmp on VDJdb full records with imputed missing chains.
tcremp_10xdcode_analysis — 10x CITE-seq + TCREmp embedding with DBSCAN epitope clustering.
Single-Cell Analysis#
single_cell_load — Load 10x VDJ v1 donors, inspect chain multiplicity, and benchmark against scirpy.
single_cell_pairing_analysis — Build and compare pairing graphs across raw, imputed, and cleaned stages.