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Sort EcoSIM run folders for a set of sites into one project directory with input/<SITE_ID>/ and run_dir/<SITE_ID>/ subdirectories and a project manifest. Use when asked to create EcoSIM run folders, runs, or cases for several sites at once ("create ecosim run folders for US-UMB, US-xGR, and US-Ha1", "set up a multi-site EcoSIM project"), or to add, refresh, or summarize sites in such a project.

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週ごとに Notion「ナレッジカード」DB に集まったカードを読み、問いをまたいで親和図にまとめ、正（worked）と反（failed）の対立から合（提案）を出し、次の問いを決めて、「合成テーマ」DB と週の行の配下の「まとめ」ページに書き込む。「今週のカードを合成して」「W43 のまとめを作って」「ナレッジカードの合成」などの依頼で使う。カードの提出は knowledge-cards、個人の採点は evaluate-session の領域。個人別の件数ランキングや「誰が何を失敗した」は出さない。

Claude Code のセッション記録（~/.claude の履歴・セッションログ・memory）から、週ごとの問い（questions.json）に答える「ナレッジカード」を下書きし、本人が確認・修正したうえで機密スキャンを通し、Notion の「ナレッジカード」DB に提出する。引数なしなら先週（月曜〜日曜）の記録を集計し、確認のうえ Notion に提出する。「Claude Code の履歴をナレッジカードにまとめて」「先週のログからナレッジカードを作って」「ナレッジカードを提出したい」「今週のカードを出して」「週次の振り返りカードを作って」などの依頼で使う。週次のカード提出であり、個人の採点や評価ではない（セッション 1 本の採点は evaluate-session の領域）。

Load and preprocess imaging mass cytometry (IMC) and MIBI data from raw MCD/TXT through hot-pixel removal, spillover compensation, and variance-stabilizing transformation, covering readimc/steinbock ingestion, NNLS spillover compensation (CATALYST), IMC-Denoise, and the IMC arcsinh-cofactor question. Use when starting analysis from raw MCD files, building per-channel TIFF stacks, compensating channel spillover, choosing an arcsinh cofactor, or preparing single-cell intensities for phenotyping.

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Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and correctness (reference-free Merqury QV, Inspector/CRAQ structural errors, asmgene false-duplication/collapse). Covers why N50 is the most-gamed metric, why QV measured on the polishing reads is circular, distinguishing uncollapsed haplotigs from real WGD, and the EBP/VGP 6.C.Q40 standard. Use when judging whether an assembly is good enough to annotate or publish, comparing assemblers, diagnosing a fragmented or duplicated assembly, or assessing a phased diploid assembly.

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Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.

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Segment single cells from multiplexed IMC/MIBI tissue images using Mesmer/DeepCell, Cellpose, or ilastik+CellProfiler, covering whole-cell vs nuclear segmentation, the summed-membrane-channel decision, nuclear-expansion bias, lateral spillover, resolution-floor parameters, and downstream-proxy evaluation. Use when delineating cells after preprocessing, choosing a segmentation model, building a cell mask for quantification, diagnosing impossible double-positive populations, or troubleshooting over/under-segmentation.

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Identify tumor neoantigens from somatic variants with pVACtools (pVACseq/pVACfuse/pVACbind/pVACvector/pVACview) for personalized cancer vaccines and checkpoint biomarkers. Encodes the field's hard truth that binding prediction is the easy, near-solved part and single-digit-percent PPV lives downstream — so it centers clonality/CCF, HLA LOH (the silent invalidator), expression, proximal-variant phasing, agretopicity/foreignness quality, and the predicted->presented->immunogenic validation tiers. Use when nominating vaccine targets, ranking neoantigens, or building a tumor-to-candidate pipeline. Binding details in mhc-binding-prediction; ranking in immunogenicity-scoring.

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Calls significant loops from protein-directed and targeted 3C assays (HiChIP, PLAC-seq, Capture Hi-C/PCHi-C, ChIA-PET) where the contact background is peak-anchored and coverage-biased, so generic Hi-C loop callers (cooltools dots, Juicer HiCCUPS) use the wrong null. Covers FitHiChIP (config-driven coverage+distance-decay spline regression, peak-to-peak vs peak-to-all foreground, loose vs stringent background, coverage vs ICE bias), MAPS (positive Poisson regression on bias factors for PLAC-seq/HiChIP), hichipper (restriction-site-distance bias model + library QC), CHiCAGO (Delaporte two-component Brownian+technical background for asymmetric bait x other-end Capture Hi-C), the with/without separate-ChIP anchor decision, and differential loops via diffloop. Use when calling loops from HiChIP/PLAC-seq/Capture Hi-C, choosing FitHiChIP/MAPS/CHiCAGO, picking peak-to-all vs peak-to-peak, setting the loop FDR, supplying ChIP peaks as anchors, QCing a HiChIP library, or comparing loops between conditions.

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Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with GenomeScope2 to estimate genome size, heterozygosity, repeat content, and ploidy, and Smudgeplot to infer ploidy from heterozygous k-mer pairs (diploid AB vs triploid AAB vs tetraploid AABB). Covers choosing k via Merqury best_k.sh, the k-mer-coverage vs sequencing-coverage confusion, reading het/repeat/contamination/organelle peaks, why noisy ONT must not be used for counting, and how the estimate becomes the NG50 denominator, the Flye -g value, the hifiasm --hom-cov/purge setting, and the 1.5-2x-too-big haplotig sanity check. Use when starting any de novo assembly, deciding whether short reads can work, estimating genome size for an unknown organism, diagnosing ploidy, or sanity-checking an assembly's size against expectation.

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Interactive cell annotation and image QC for IMC/MIBI using napari, napari-imc, Mantis Viewer, and cytomapper, covering the pixels-to-cell-table bridge, overlaying masks to catch segmentation/spillover artifacts, inter-annotator variability as the accuracy ceiling, contrast-as-threshold, and building class-balanced ground-truth label sets. Use when manually labeling cells, generating training data for a classifier, QC-ing segmentation on the image, confirming clusters are spatially real, or choosing an annotation viewer.

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Infer or annotate TCR antigen specificity by unsupervised clustering (TCRdist/tcrdist3, GLIPH2, clusTCR, GIANA) and database lookup (VDJdb, IEDB, McPAS-TCR), and rank candidates with supervised predictors (ERGO-II, NetTCR-2.x, pMTnet) under explicit caveats. Encodes the central truth that general TCR-epitope prediction for UNSEEN epitopes essentially does not work (collapses to near-random; IMMREP22, Grazioli 2022) because labeled data is dominated by a few immunodominant epitopes and there is no true negative set — so clustering for discovery is the honest task and de-novo binding needs wet-lab validation. Use when annotating TCR specificity or grouping a repertoire. Epitope/MHC context lives in mhc-binding-prediction.

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Rank and prioritize neoantigen/epitope candidates by likely T-cell response using NeoFox feature annotation, PRIME2.0, BigMHC-IM, the Łuksza/Balachandran fitness model (agretopicity + foreignness), and pVACtools tiering. Encodes the field's hard truths that immunogenicity is the least-solved layer (dedicated scores ~AUROC 0.6-0.7, modest PPV), that scores are valid only for RANKING within one patient (never absolute go/no-go or cross-patient), that DAI has anchor-inflation and WT-denominator traps, and that stacking weak correlated scores into one number is a red flag. Use when ordering a candidate list for a vaccine. Binding lives in mhc-binding-prediction; calling in neoantigen-prediction.

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Compare cell-type composition and spatial features across conditions in IMC/MIBI cohorts with the patient as the experimental unit, covering pseudoreplication, per-patient aggregation, mixed models, compositional (Dirichlet/scCODA) differential abundance, diffcyt, per-image-to-patient spatial differential testing (SpaceANOVA), batch covariates, and FDR. Use when testing whether a cell type or spatial niche differs between groups, avoiding cell-level pseudoreplication, choosing a differential-abundance method, or correctly powering an IMC cohort comparison.

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Assign cell types from marker expression in IMC/MIBI data using clustering (PhenoGraph/FlowSOM/Leiden/Pixie), marker-based probabilistic classifiers (Astir), or image-context CNNs (CellSighter), covering the double-positive segmentation artifact, lineage-vs-state markers, the two spillover types, and why a "cell type" in imaging is conditioned on a segmentation guess. Use when phenotyping segmented IMC cells, choosing clustering vs classification, diagnosing implausible double-positive populations, separating lineage from functional markers, or transferring labels across a cohort.

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Detects TAD boundaries from balanced Hi-C contact matrices via the diamond-window insulation score (cooltools insulation) and HiCExplorer hicFindTADs, returning a continuous log2 insulation track, valley-prominence boundary_strength, and Li/Otsu-thresholded is_boundary flags across a list of window sizes. Covers the multi-scale window sweep (sub-TAD to compartment-domain), why the boundary is reproducible but the domain partition is not, cross-condition comparison via differential SCORE not differential partition, and the insulation-vs-compartment orthogonality. Use when calling TADs or domain boundaries, computing insulation scores, choosing a window size, ranking boundary strength, comparing boundaries across conditions, or annotating CTCF-backed boundaries; route domain rendering to hic-visualization and boundary-feature overlap to genome-intervals.

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Assembles haplotype-resolved diploid and telomere-to-telomere (T2T) genomes from PacBio HiFi reads with hifiasm (HiFi-only, Hi-C, or trio phasing) and verkko (HiFi + ultralong ONT for T2T), extracting contigs from GFA and routing phasing QC to k-mer/trio metrics. Covers why a primary assembly is a haplotype mosaic that exists in no cell, partial-vs-full phasing (the .bp. vs .dip. filename convention), the purge-default trap on inbred samples, the --hom-cov coverage-estimate alarm, and verkko-vs-hifiasm for T2T. Use when assembling a diploid eukaryote from HiFi, phasing haplotypes with parents (trio) or Hi-C, deciding whether to chase T2T, or diagnosing switch errors invisible to N50/BUSCO/QV.

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Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.

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Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.

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Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) with pyBigWig (Python) and the UCSC Kent tools (bedGraphToBigWig, bigWigToBedGraph, bigWigInfo, bigWigSummary, bigWigAverageOverBed) and deepTools (multiBigwigSummary, computeMatrix, bigwigCompare). Covers the central trap that a wide query returns a precomputed zoom-level summary (by default the mean, which annihilates narrow peaks) not per-base data, when exact=True/values() is mandatory, the NaN-not-zero gap-handling fork, choosing mean vs max vs sum vs coverage by biological question, and the sorted-bedGraph plus chrom.sizes build requirement. Use when extracting signal at regions, computing mean signal per gene/peak, building a browser track from bedGraph, comparing tracks, or building TSS/gene-body metaprofiles.

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Assembles microbial-community sequencing into metagenome-assembled genomes (MAGs) with metaFlye (ONT), metaSPAdes/MEGAHIT (Illumina), and hifiasm-meta/metaMDBG (PacBio HiFi), then recovers genomes via multi-binner consolidation (MetaBAT2, MaxBin2, CONCOCT, SemiBin2, VAMB -> DAS_Tool) and QCs them against MIMAG with CheckM2, GUNC, and GTDB-Tk. Covers why a metagenome is not a genome (uneven coverage, micro-diversity, strain collapse to consensus), differential-coverage binning, co-assembly vs per-sample, the rRNA-operon collapse that fails short-read MAGs, and strain resolution with inStrain. Use when reconstructing genomes from a microbiome, soil, ocean, or gut community, recovering MAGs, or resolving strain-level variation.

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Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap spacers (adds no sequence). Covers Hi-C/Omni-C scaffolding (YaHS, SALSA2, 3D-DNA/Juicer), Hi-C read-mapping prerequisites (map each end separately, no mate rescue, dedup, enzyme-aware), reading the contact map for misjoins/inversions/false-duplications, manual curation in Juicebox/PretextView (the VGP/DToL standard), reference-guided scaffolding (RagTag) and its karyotype-erasure hazard, genetic-map (ALLMAPS) and Bionano optical-map integration, chimera-breaking before scaffolding, gap-filling, and telomere/contig-vs-scaffold-N50 QC (tidk). Use when turning contigs into chromosomes with Hi-C, integrating a linkage map or optical map, choosing a scaffolder by available linking data, or judging whether a chromosome-scale assembly is trustworthy.

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Designs pegRNAs and nicking guides for prime editing (PE) -- choosing the nick/strand, tuning the primer-binding site (PBS) and reverse-transcription template (RTT) as a per-locus panel, selecting the PE system (PE2/PE3/PE3b/PE4/PE5/PEmax/PE7), adding MMR-evading and PAM-disrupting silent edits, appending epegRNA 3' motifs (tevopreQ1/mpknot), and ranking with PRIDICT/DeepPrime. Covers twinPE/PASTE for large insertions and the prime-vs-base-editing decision. Use when designing a scarless point mutation, small insertion/deletion, or any of the 12 base conversions without a double-strand break, when efficiency is low and MMR inhibition or pegRNA stabilization is needed, or when routing a large insertion to an integrase method. Generic guide scoring and base editing are separate skills.

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Tests whether two genomic interval sets overlap (colocalize) more than expected by chance using a permutation test against a structured-genome null model. Covers bedtools fisher (analytic 2x2 screen), bedtools shuffle + jaccard permutation, GAT (isochore/GC-conditioned simulation with FDR), regioneR (flexible permutation, randomizeRegions vs circularRandomizeRegions, localZScore), LOLA (universe-relative Fisher against a region database), and GREAT/rGREAT (regulatory-domain binomial + hypergeometric for ontology-from-regions). Stresses the universe/background choice, matched background, blacklist exclusion, and multiple-testing control. Use when asking whether peaks/regions are enriched at enhancers/TFBS/features, scoring region-set colocalization or region-set enrichment, comparing CNV/SV concordance, or turning an overlap count into a defensible p-value.

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