Tags
The inverse of the chips on each page — every tag in use, and what carries it. Tags are
grouped into facets (Meta, Family, Role, Domain, Topic) and validated against meta_tags.yml, which
documents every one of them. 37 tags in use across the corpus.
Family
Which side of the analyze/referee split a Mold sits on (glossary Family A / Family B).
Role
The Family-A or Family-B role a Mold plays (glossary construct/critique/calibrate).
Domain
Subject-matter area a Mold/note applies to. Closed enum — add a documented row per domain.
- domain/ancestral-reconstruction 9 entriesInferring ancestral sequence/character states across a phylogeny.
- domain/batch-effects 18 entriesTechnical, non-biological variation that confounds measured signal.
- domain/clustering 1 entryUnsupervised grouping into discrete categories; distance choice and cluster validation.
- domain/comparative-annotation 4 entriesProjecting/transferring gene annotations across genomes (liftover, CESAR, TOGA, CAT, Liftoff).
- domain/data-visualization 1 entryConstructing honest exploratory/publication data displays; artifacts of scale, smoothing, ordering.
- domain/differential-expression 7 entriesTesting expression/abundance differences (RNA-seq, microarray, methylation).
- domain/dimensionality-reduction 2 entriesOrdination / low-dimensional embedding of high-dim data (PCA, SVD, MDS, t-SNE).
- domain/experimental-design 9 entriesSample allocation, blocking, and randomization decided before data collection.
- domain/gene-family-evolution 10 entriesGene gain/loss/duplication dynamics across lineages.
- domain/image-analysis 1 entryTurning digital images into quantitative measurements: segmentation, filtering, feature extraction.
- domain/molecular-evolution 17 entriesSequence change over evolutionary time (substitution, selection).
- domain/pangenomics 10 entriesAnalysis across a species' full core/accessory gene complement.
- domain/phylogenetic-comparative-methods 17 entriesTrait evolution and diversification inferred on a fixed phylogeny (PGLS, BiSSE/HiSSE).
- domain/phylogenetics 4 entriesInferring evolutionary trees from molecular data.
- domain/single-cell-genomics 3 entriesSingle-cell / droplet assays (demultiplexing, hashing, count-splitting, cluster inference).
- domain/spatial-statistics 1 entrySpatial point patterns vs a complete-spatial-randomness baseline (point processes, Ripley's K).
- domain/statistical-inference 17 entriesGeneral validity of statistical inference — multiple testing, post-selection, confounding, reproducibility.
- domain/supervised-learning 1 entryLearning a predictive rule from labeled data while guarding against overfitting.
- domain/synteny 5 entriesConserved gene order / collinearity across genomes (MCScanX, SyRI, GENESPACE).
- domain/whole-genome-alignment 9 entriesGenome-to-genome alignment / homology mapping (Cactus, HAL, minimap2, MUMmer, chain/net).
- domain/whole-genome-duplication 5 entriesPolyploidy / WGD detection via Ks distributions and duplicate retention.
Topic
Finer-grained subject beneath a domain. Closed enum — add a documented row per topic.
- topic/confounding 12 entriesBatch / surrogate-variable / collider confounding of a biological contrast.
- topic/dnds 8 entriesNonsynonymous/synonymous substitution-rate ratio; a test for selection (under molecular-evolution).
- topic/gc-biased-gene-conversion 2 entriesgBGC as a confound of selection signals.
- topic/ks-distribution 3 entriesKs-based WGD dating / substitution saturation.
- topic/liftover 3 entriesCoordinate/annotation liftover across assemblies.
- topic/multiple-testing 7 entriesFWER/FDR control across many simultaneous tests.
- topic/pangenome-openness 6 entriesOpen/closed pangenome; core/accessory dynamics.
- topic/positive-selection 10 entriesCodon-model tests for positive selection (BUSTED/MEME/aBSREL/branch-site).
- topic/post-selection-inference 6 entriesDouble-dipping / selective inference / count-splitting.
- topic/recombination 2 entriesRecombination detection (e.g. GARD) affecting selection inference.
- topic/reproducibility 5 entriesForking paths, p-hacking, researcher degrees of freedom.