2.5万 件 ・ 関連度順
概要と使いどころ
Guides agents through scorecards, outcomes, model profiles, and eval suites. Use when running /cc-scorecard or /cc:scorecard, measuring a deliverable, or checking workflow gates with suite-run.
日本語の概要は準備中です。原文の説明を表示しています。
Provides expert knowledge for building Astro 5+ sites with Islands Architecture, Content Collections, TypeScript, and performance-first rendering strategies.
日本語の概要は準備中です。原文の説明を表示しています。
Add or modify a Flask endpoint in the Lyrion Dashboard. Use this whenever a task adds a new URL/route, a JSON API endpoint, or a page — anything that registers a handler in `routes/`. Covers the repo's route → service → test layering, input validation, caching headers, security headers, i18n wiring, and the exact test pattern, so a new endpoint matches how `routes/` already works instead of reinventing the structure.
日本語の概要は準備中です。原文の説明を表示しています。
Add, change, or translate user-facing text in the Lyrion Dashboard, which ships bilingual FR/EN. Use this whenever a task introduces a new visible string (a label, tooltip, aria-label, empty state, stat name), changes wording, or touches the README or a `docs/` page — so every string lands in both languages and the EN/FR documentation pairs stay in sync. Covers `i18n.py`, how templates and JS consume translations, and the parity rule.
日本語の概要は準備中です。原文の説明を表示しています。
Write or fix a test in the Lyrion Dashboard's suite. Use this whenever a task adds a test, changes one, or asks why the suite fails — anything touching `tests/`. Covers the standalone-per-file scaffolding, the env-before-import rule, where to patch (the route/service the code under test imports), the cache-and-clock testing pattern, and how to run one test vs the whole suite. Reach for it any time you touch `tests/` so new tests match the existing shape instead of re-inventing setup.
日本語の概要は準備中です。原文の説明を表示しています。
Work on the dashboard's frontend — the vanilla JS/CSS page with no framework or bundler. Use this whenever a task touches `static/nowplaying.js`, `static/style.css`, the Jinja templates (`templates/nowplaying.html`, `_icons.html`), the accent-color tinting, the karaoke lyrics sync, the now-playing poll, or the empty-state mosaic / recent-plays pile. Covers how the page is wired, how it reads i18n and data from the server, the ESLint gate, and the Android bridge, so changes match the existing patterns.
日本語の概要は準備中です。原文の説明を表示しています。
Work on the Android app — the thin WebView wrapper in `android/`. Use this whenever a task touches the Kotlin sources, the Gradle build, the WebView shell, the native settings screen, LMS server auto-discovery, the JS↔native bridge, app strings/i18n, or the Android CI/lint. Covers the "shell only, UI lives on the web" principle, the debug/release signing split, the static versioning F-Droid needs, and the min/target SDKs, so changes fit the wrapper.
日本語の概要は準備中です。原文の説明を表示しています。
Read data from Lyrion's SQLite databases — library stats, stored lyrics, album covers, recent plays. Use this whenever a task queries `library.db` or `persist.db`, adds or changes a statistic, or touches `services/database.py`. Covers the read-only connection model (RO open + `ATTACH persist.db`), the key tables, the `play_counts` view over the Alternative Play Count plugin, the single-flight stats cache, and why the app must never write to these DBs. Reach for it before writing any SQL against the Lyrion databases.
日本語の概要は準備中です。原文の説明を表示しています。
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）。
DeepSeek HarnessのWeb版・公式Desktop版の会話や設定を操作する。対象インスタンスを特定し、認証済みHTTP RPCまたはアプリ画面で読取・依頼・追記・中断を行う。既存チャットの操作をheadlessの別実行と取り違えない。
Predict peptide-MHC class II (HLA-DR/DQ/DP) binding and presentation for CD4 T-cell epitopes with NetMHCIIpan-4.3 and MixMHC2pred-2.0. Covers why class II is far less reliable than class I (open binding groove, 9-mer register ambiguity, sparse noisy training data, DR>DP>DQ accuracy asymmetry), the DQ/DP heterodimer alpha/beta pairing trap, and the looser 1%/5% %Rank thresholds. Use when predicting CD4 epitopes for vaccine help, mapping class II neoantigens, or scoring long peptides against DR/DQ/DP. For CD8/class I see mhc-binding-prediction.
日本語の概要は準備中です。原文の説明を表示しています。
Annotates bacterial and archaeal genomes (isolates, MAGs, plasmids) with Bakta (active versioned databases, NCBI-compliant output) or Prokka (legacy), producing GFF3/GenBank/EMBL/FASTA with INSDC locus tags. Covers Bakta-vs-Prokka-vs-PGAP-vs-DFAST choice, light-vs-full database tiers, translation-table selection (11/4/25), archaeal and leaderless-gene caveats, the small-ORF blind spot, pseudogene-vs-phase-variation, the pangenome re-annotation trap, and submission compliance. Use when annotating a newly assembled prokaryotic genome, choosing an annotation tool, re-annotating a collection for pangenomics, or preparing annotations for NCBI/DDBJ submission.
日本語の概要は準備中です。原文の説明を表示しています。
Discovers, classifies, and masks repetitive elements and transposable elements with RepeatModeler2 (de novo family library), RepeatMasker (masking against a library), EDTA (plant/structural TEs), or EarlGrey (auto-curating wrapper), and quantifies TE expression from RNA-seq with TEtranscripts/SQuIRE. Covers de-novo-library-as-curation-project, soft-vs-hard masking, the domesticated-gene over-masking massacre, Dfam-vs-RepBase, TE classification (Class I/II, family-vs-copy), Kimura repeat landscapes, LAI, and the RNA-seq multimapping problem. Use when masking repeats before gene prediction, building a TE library for a non-model genome, or analyzing transposable-element content or expression.
日本語の概要は準備中です。原文の説明を表示しています。
Assigns GO terms, Pfam/InterPro domains, KEGG orthologs, EC numbers, and product names to predicted proteins using eggNOG-mapper (orthology), InterProScan (domain signatures), and KofamScan (KEGG), routing specialized functions to dbCAN/antiSMASH/AMRFinderPlus/SignalP. Covers the orthology-vs-domain-vs-homology paradigms, the annotation-error percolation cascade, domain-presence-is-not-function, GO IEA circularity in enrichment, evidence tiering, and bit-score/coverage thresholds. Use when adding functional annotation to predicted genes, choosing between eggNOG-mapper and InterProScan, or judging how much to trust a functional label.
日本語の概要は準備中です。原文の説明を表示しています。
Decides whether and how to polish a draft genome assembly to raise consensus accuracy (QV) with read-type-matched tools - Racon and medaka (ONT consensus), dorado polish, Polypolish and pypolca (Illumina, repeat-aware), Pilon (legacy short-read), NextPolish/NextPolish2, Hapo-G (haplotype-aware), ntEdit, and DeepPolisher/PEPPER-Margin-DeepVariant for human. Covers the do-not-polish-HiFi rule, the medaka basecaller-model footgun, held-out Merqury QV as the only honest stop signal, and the haplotype-collapse trap. Use when correcting homopolymer indels or residual SNPs in a long-read assembly, deciding if a HiFi assembly needs polishing, or choosing an ONT vs hybrid vs short-read polishing chain.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
Computes and interprets sequencing read depth and coverage over a genome, windows, or target regions with mosdepth (windowed depth, cumulative distribution, --quantize callable BEDs), bedtools genomecov/coverage (bedGraph tracks, per-target stats), samtools depth/coverage (per-base depth, per-contig depth+breadth). Covers the breadth-vs-mean distinction, the cumulative-coverage curve, evenness (CV/Fano/fold-80/Gini), what each tool silently counts (duplicates, secondary/supplementary, MAPQ, read span vs fragment, mate-overlap), the samtools-depth 8000-cap version trap, and the bedtools coverage -a/-b orientation flip. Use when assessing sequencing adequacy, building coverage tracks, computing breadth at a depth threshold, defining callable regions, or QCing target-capture uniformity.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
Balances Hi-C contact matrices (ICE via cooler.balance_cooler, KR/SCALE/VC context), computes distance-decay expected with cooltools (expected_cis per-diagonal P(s), expected_trans scalar), builds observed/expected (O/E) matrices, and diagnoses polymer state from the P(s) log-derivative. Covers the within-matrix-vs-cross-sample distinction (balancing is NOT a normalizer), the equal-visibility assumption that CNV/aneuploidy violates (use raw counts for copy-number), cis-only balancing, mad_max/blacklist masking before balancing, multiplicative cooler weights vs divisive juicer weights, and the resolution-vs-depth budget. Use when balancing a .cool/.mcool, computing expected or P(s), making O/E matrices for compartments/loops, deciding ICE vs KR vs SCALE, choosing a resolution for a given depth, or troubleshooting NaN/all-NaN balanced matrices; route cross-sample comparison to hic-differential.
日本語の概要は準備中です。原文の説明を表示しています。
Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using cooler (Python + CLI), hic2cool, and hictk. Covers the single-resolution mcool URI (file.mcool::/resolutions/<bp>), the load-bearing divisive-vs-multiplicative weight-naming rule (KR/VC/VC_SQRT auto-divisive vs cooler's multiplicative weight), what survives .hic<->.cool conversion (FRAG matrices and norm vectors do not), raw-vs-balanced coarsening, the .pairs upper-triangle/chromsize-order contract, and chrom-naming/bin-table provenance. Use when loading a cooler, converting .hic to .mcool, selecting a resolution, building a cooler from pairs or a matrix, coarsening/zoomifying, importing Juicer norm vectors, or debugging all-NaN balanced matrices and chr1-vs-1 empty fetches.
日本語の概要は準備中です。原文の説明を表示しています。
Designs donor/repair templates for precise CRISPR knock-ins -- choosing the format (ssODN, long-ssDNA/Easi-CRISPR, dsDNA/plasmid, AAV6), sizing homology arms, placing the cut within ~10 bp of the edit, and adding a mandatory codon-checked blocking (PAM/seed) mutation so the edited allele is not re-cut. Frames the HDR-vs-NHEJ-vs-MMEJ pathway competition, the MMEJ (PITCh) and homology-independent (HITI/HMEJ) alternatives for post-mitotic cells, ssODN strand/asymmetry choice, phosphorothioate end-protection, and ranked HDR enhancers. Use when designing a donor for a point mutation, epitope/fluorophore tag, allele replacement, or knock-in, or when HDR efficiency is low. Guide design and base/prime editing are separate skills.
日本語の概要は準備中です。原文の説明を表示しています。