「sec」の検索結果

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.

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。

Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM; Liu 2022 *NAR Genom Bioinform* 4:lqac046), MeTPeak (HMM over sliding windows; Cui 2016 *Bioinformatics* 32:i378), MACS3 / MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment confirmation via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output formats, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union; cross-caller IDR-equivalent), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody-based methods cannot resolve, and orthogonal-validation routes (miCLIP / GLORI / m6A-SAC-seq / m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set as a whole, reconciling differing peak sets across tools, validating MeRIP peaks against orthogonal single-base methods, interpreting peaks at the 5' end where m6Am contamination is possible, or recommending a multi-tool consensus strategy.

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。

Build UpSet plots to visualize set intersections beyond 4 sets (where Venn fails) using ComplexUpset (modern, ggplot2-grammar) or the unmaintained UpSetR, with explicit cardinality vs degree sorting, attribute panels, and query highlighting. Use when comparing overlap across many gene sets, peak sets, variant lists, or any set membership matrix where Venn diagrams become illegible.

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。

Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.

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。

Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.

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。

Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.

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。

Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.

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。

Implements missing-data sensitivity analyses for confirmatory clinical trials including MMRM under MAR (with Kenward-Roger correction), reference-based multiple imputation (J2R, CR, CIR, LMCF per Carpenter-Roger 2013), Permutt delta-adjustment / tipping-point analysis, pattern-mixture identifying restrictions (CCMV, NCMV, ACMV), and the Cro vs Bartlett variance debate. Use when handling missing primary or secondary endpoint data in regulatory submissions following NRC 2010 and ICH E9(R1).

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。

Compact the session into gitignored `.codeconductor/sessions/handoff.md` (redact secrets).

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 REST API design standards and best practices for Spring Boot projects. Use when creating or reviewing REST endpoints, DTOs, error handling, pagination, security headers, HATEOAS and architecture 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。

Verification loop for Spring Boot projects: build, static analysis, tests with coverage, security scans, and diff review before release or PR.

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 patterns to generate comprehensive REST API documentation using SpringDoc OpenAPI 3.0 and Swagger UI in Spring Boot 3.x applications. Use when setting up API documentation, configuring Swagger UI, adding OpenAPI annotations, implementing security documentation, or enhancing REST endpoints with examples and schemas.

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。

Analyze suspicious artifacts in an isolated lab to contain and recover. For incident responders on owned estates. Never write, improve, or distribute malware.

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。

Plan and report authorized vulnerability assessments on owned systems. Prioritize evidence, severity, and remediations. Do not deliver exploit payloads.

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。

Hunt for adversary techniques in telemetry you are authorized to query. Hypothesis-driven, evidence-first, no live offensive operations.

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 patterns to configure Spring Boot Actuator for production-grade monitoring, health probes, secured management endpoints, and Micrometer metrics across JVM services. Use when setting up monitoring, health checks, or metrics for Spring Boot applications.

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。

Harden network architecture, segmentation, TLS, and allowlists for systems you operate. Defensive design and review only.

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。

Automate detection, enrichment, and response playbooks for a SOC you operate. Keep humans in the loop for destructive actions.

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。

Understand how a confirmed vulnerability in an owned system is triggered so you can patch and test it. This is not exploit development for offense. No payloads, malware, or attack procedures.

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。

Harden IAM, storage, keys, and org policies in cloud accounts you administer. Focus on identity, logging, and public-exposure controls.

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。

Map controls to SOC2, ISO 27001, PCI, or internal policy for the org you work for. Evidence and control design — not audit theater.

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。

Improve detections, hardening, and response for the estate you defend. Detection-as-code and control design, not offense.

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。

Harden iOS/Android apps you ship: storage, TLS pinning policy, IPC, and backend trust. You still enforce authz on the server.

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。

Plan purple-team / adversary-simulation exercises against systems you are contracted to test. High-level objectives and detection gaps only. No live attack procedures or payloads.

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。