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Guide users through writing a systematic literature review (SLR) following the PRISMA 2020 framework. Use this skill whenever the user mentions 'systematic review', 'systematic literature review', 'SLR', 'PRISMA', 'PRISMA 2020', 'PRISMA flow diagram', 'PRISMA checklist', or asks for help writing, structuring, or auditing a literature review that follows reporting guidelines. Also trigger when the user asks about inclusion/exclusion criteria for a review, search strategies for databases like Scopus/WoS/PubMed, study selection processes, risk of bias assessment, or narrative synthesis for a review paper. This skill covers the full PRISMA 2020 checklist (27 items), produces a Word document manuscript in strict journal article format, generates an annotated PRISMA flow diagram, and enforces APA 7th Edition referencing throughout. It does NOT cover meta-analysis or statistical pooling. By Chuah Kee Man.

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 and maintain a Stockbee-style daily 20% mover study for US equities by scanning +20%/-20% movers, classifying catalysts and setup context, updating forward outcomes, and summarizing cohort patterns. Use when the user asks to run a daily 20% study, backfill historical 20% movers, find recurring edge patterns, or build a model book of explosive market moves.

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 and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Nat Commun 12:1302), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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。

Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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。

Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2020 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer 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。

Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Cell Reports 36:109597), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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。

Web 线上展览开发 (虚拟展厅) (Web 线上展览 / 虚拟展厅开发 (从业者/工程视角) — 用 web 技术开发线上展览、虚拟展厅、云展会、数字展馆，覆盖 3D 空间、全景漫游、WebXR、文博数字化、营销云展厅、3D 商品展示等形态。覆盖: (a) 技术栈 — 3D web(Three.js / React Three Fiber / Babylon.js / Google model-viewer / WebGL / WebGPU)、全景(Pannellum / Marzipano / Photo Sphere Viewer / krpano / 720云)、WebXR(WebXR Device API / A-Frame)、资产管线(glTF·GLB / Draco / Meshopt / KTX2 纹理压缩 / gltf-transform / LOD); (b) 自研 vs SaaS 平台选型(国内: 众趣 / 酷雷曼 / 比目鱼 / 会鸽 / 3DVista; 海外: Matterport / Kuula / Artsteps / Spatial); (c) 性能优化(大场景加载 / 模型轻量化 / draw call / 移动端 / 首屏 / 显存)——web 3D 第一性难题; (d) 策展与导览(动线设计 / 热点 hotspot / 语音讲解 / 交互); (e) 文博数字化(IIIF / 数字孪生 / 高清文物) 与 会展·电商商业化(营销云展厅 / 数据埋点 / 线索转化); (f) 部署(CDN / 流式加载 / 跨端兼容 / WebGL 降级)。学派分歧: 自研 Three.js vs SaaS 平台、真 3D 重场景 vs 720 全景轻量、WebGL vs WebGPU、文博考据派 vs 营销转化派、沉浸优先 vs 加载优先。不含: 线下展陈 / 展台搭建、原生 VR App(非 web)、通用 3D 游戏开发、纯 3D 建模教程。) Master OS — automated mastery of Web 线上展览 / 虚拟展厅开发 (从业者/工程视角) — 用 web 技术开发线上展览、虚拟展厅、云展会、数字展馆，覆盖 3D 空间、全景漫游、WebXR、文博数字化、营销云展厅、3D 商品展示等形态。覆盖: (a) 技术栈 — 3D web(Three.js / React Three Fiber / Babylon.js / Google model-viewer / WebGL / WebGPU)、全景(Pannellum / Marzipano / Photo Sphere Viewer / krpano / 720云)、WebXR(WebXR Device API / A-Frame)、资产管线(glTF·GLB / Draco / Meshopt / KTX2 纹理压缩 / gltf-transform / LOD); (b) 自研 vs SaaS 平台选型(国内: 众趣 / 酷雷曼 / 比目鱼 / 会鸽 / 3DVista; 海外: Matterport / Kuula / Artsteps / Spatial); (c) 性能优化(大场景加载 / 模型轻量化 / draw call / 移动端 / 首屏 / 显存)——web 3D 第一性难题; (d) 策展与导览(动线设计 / 热点 hotspot / 语音讲解 / 交互); (e) 文博数字化(IIIF / 数字孪生 / 高清文物) 与 会展·电商商业化(营销云展厅 / 数据埋点 / 线索转化); (f) 部署(CDN / 流式加载 / 跨端兼容 / WebGL 降级)。学派分歧: 自研 Three.js vs SaaS 平台、真 3D 重场景 vs 720 全景轻量、WebGL vs WebGPU、文博考据派 vs 营销转化派、沉浸优先 vs 加载优先。不含: 线下展陈 / 展台搭建、原生 VR App(非 web)、通用 3D 游戏开发、纯 3D 建模教程。: top builders' mental models, tool stack, current workflows, jargon, and where to keep up. Trigger this skill when the user works on Web 线上展览 / 虚拟展厅开发 (从业者/工程视角) — 用 web 技术开发线上展览、虚拟展厅、云展会、数字展馆，覆盖 3D 空间、全景漫游、WebXR、文博数字化、营销云展厅、3D 商品展示等形态。覆盖: (a) 技术栈 — 3D web(Three.js / React Three Fiber / Babylon.js / Google model-viewer / WebGL / WebGPU)、全景(Pannellum / Marzipano / Photo Sphere Viewer / krpano / 720云)、WebXR(WebXR Device API / A-Frame)、资产管线(glTF·GLB / Draco / Meshopt / KTX2 纹理压缩 / gltf-transform / LOD); (b) 自研 vs SaaS 平台选型(国内: 众趣 / 酷雷曼 / 比目鱼 / 会鸽 / 3DVista; 海外: Matterport / Kuula / Artsteps / Spatial); (c) 性能优化(大场景加载 / 模型轻量化 / draw call / 移动端 / 首屏 / 显存)——web 3D 第一性难题; (d) 策展与导览(动线设计 / 热点 hotspot / 语音讲解 / 交互); (e) 文博数字化(IIIF / 数字孪生 / 高清文物) 与 会展·电商商业化(营销云展厅 / 数据埋点 / 线索转化); (f) 部署(CDN / 流式加载 / 跨端兼容 / WebGL 降级)。学派分歧: 自研 Three.js vs SaaS 平台、真 3D 重场景 vs 720 全景轻量、WebGL vs WebGPU、文博考据派 vs 营销转化派、沉浸优先 vs 加载优先。不含: 线下展陈 / 展台搭建、原生 VR App(非 web)、通用 3D 游戏开发、纯 3D 建模教程。 problems and wants industry-grade thinking, tool selection, or workflow guidance. 触发词：「线上展览」「虚拟展厅」「web 线上展览」「云展厅」「数字展馆」

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。

K12 体育培训 (K12 / 青少年体育培训 (从业者视角) — 面向 3-18 岁青少年的校外体育培训生意，政策改革驱动的高增长赛道。覆盖: (a) 业态分层 — 少儿体适能 (3-12 岁基础运动能力/感统/协调) vs 专项培训 (篮球/游泳/跳绳/羽毛球/网球/击剑/武术等单项技能) vs 中考体育备考 (初中冲刺，按各地体育中考考纲提分); (b) 政策脊椎 — 双减 (2021 教育部「双减」: 学科类压减、非学科类规范) 把体育从「兴趣班」推成刚需，体育中考分值改革 (云南/北京/各省把分值提到 50-100 分) 制造确定性需求，《国家学生体质健康标准》+《义务教育体育与健康课程标准 (2022 版)》是教学纲领; (c) 单店模型与连锁扩张 — 坪效/师生比/续费率/转介绍率/课消，直营 vs 加盟，社区店 vs Mall 店 vs 进校 (课后服务/课后三点半); (d) 教研与师资 — 课程体系标准化 (分龄分级)、教练认证 (社会体育指导员/各单项协会教练员/中国少儿体适能等)、教练「能打 ≠ 能教」断层; (e) 运营 SOP — 招生获客 (地推/社群/试听转化)、排课与场地利用率、家长沟通与续费、安全与运动损伤防控/保险; (f) 中考体育教研 — 考纲拆解 (耐力跑/跳绳/引体/坐位体前屈/球类技能)、提分训练计划、体测数据追踪。学派分歧: 体适能通识派 vs 专项技能派、中考应试提分派 vs 长期运动素养派、直营重模型 vs 加盟轻扩张、进校 (toB/课后服务) vs 校外门店 (toC)、引进体系 (如美国 SPARK/体适能认证) vs 本土自研课程。不含: 竞技体校/专业运动员青训选材深水区、成人健身/私教 (见 personal-trainer)、学科类教培、纯体育用品零售。) Master OS — automated mastery of K12 / 青少年体育培训 (从业者视角) — 面向 3-18 岁青少年的校外体育培训生意，政策改革驱动的高增长赛道。覆盖: (a) 业态分层 — 少儿体适能 (3-12 岁基础运动能力/感统/协调) vs 专项培训 (篮球/游泳/跳绳/羽毛球/网球/击剑/武术等单项技能) vs 中考体育备考 (初中冲刺，按各地体育中考考纲提分); (b) 政策脊椎 — 双减 (2021 教育部「双减」: 学科类压减、非学科类规范) 把体育从「兴趣班」推成刚需，体育中考分值改革 (云南/北京/各省把分值提到 50-100 分) 制造确定性需求，《国家学生体质健康标准》+《义务教育体育与健康课程标准 (2022 版)》是教学纲领; (c) 单店模型与连锁扩张 — 坪效/师生比/续费率/转介绍率/课消，直营 vs 加盟，社区店 vs Mall 店 vs 进校 (课后服务/课后三点半); (d) 教研与师资 — 课程体系标准化 (分龄分级)、教练认证 (社会体育指导员/各单项协会教练员/中国少儿体适能等)、教练「能打 ≠ 能教」断层; (e) 运营 SOP — 招生获客 (地推/社群/试听转化)、排课与场地利用率、家长沟通与续费、安全与运动损伤防控/保险; (f) 中考体育教研 — 考纲拆解 (耐力跑/跳绳/引体/坐位体前屈/球类技能)、提分训练计划、体测数据追踪。学派分歧: 体适能通识派 vs 专项技能派、中考应试提分派 vs 长期运动素养派、直营重模型 vs 加盟轻扩张、进校 (toB/课后服务) vs 校外门店 (toC)、引进体系 (如美国 SPARK/体适能认证) vs 本土自研课程。不含: 竞技体校/专业运动员青训选材深水区、成人健身/私教 (见 personal-trainer)、学科类教培、纯体育用品零售。: top builders' mental models, tool stack, current workflows, jargon, and where to keep up. Trigger this skill when the user works on K12 / 青少年体育培训 (从业者视角) — 面向 3-18 岁青少年的校外体育培训生意，政策改革驱动的高增长赛道。覆盖: (a) 业态分层 — 少儿体适能 (3-12 岁基础运动能力/感统/协调) vs 专项培训 (篮球/游泳/跳绳/羽毛球/网球/击剑/武术等单项技能) vs 中考体育备考 (初中冲刺，按各地体育中考考纲提分); (b) 政策脊椎 — 双减 (2021 教育部「双减」: 学科类压减、非学科类规范) 把体育从「兴趣班」推成刚需，体育中考分值改革 (云南/北京/各省把分值提到 50-100 分) 制造确定性需求，《国家学生体质健康标准》+《义务教育体育与健康课程标准 (2022 版)》是教学纲领; (c) 单店模型与连锁扩张 — 坪效/师生比/续费率/转介绍率/课消，直营 vs 加盟，社区店 vs Mall 店 vs 进校 (课后服务/课后三点半); (d) 教研与师资 — 课程体系标准化 (分龄分级)、教练认证 (社会体育指导员/各单项协会教练员/中国少儿体适能等)、教练「能打 ≠ 能教」断层; (e) 运营 SOP — 招生获客 (地推/社群/试听转化)、排课与场地利用率、家长沟通与续费、安全与运动损伤防控/保险; (f) 中考体育教研 — 考纲拆解 (耐力跑/跳绳/引体/坐位体前屈/球类技能)、提分训练计划、体测数据追踪。学派分歧: 体适能通识派 vs 专项技能派、中考应试提分派 vs 长期运动素养派、直营重模型 vs 加盟轻扩张、进校 (toB/课后服务) vs 校外门店 (toC)、引进体系 (如美国 SPARK/体适能认证) vs 本土自研课程。不含: 竞技体校/专业运动员青训选材深水区、成人健身/私教 (见 personal-trainer)、学科类教培、纯体育用品零售。 problems and wants industry-grade thinking, tool selection, or workflow guidance. 触发词：「K12 体育培训」「青少年体育培训」「少儿体适能」「中考体育」「体育中考」

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 and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Nat Commun 12:1302), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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。

Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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。

7人の専門家による多角的レビューを経て、法的リスクを最小化した取引基本契約書を対話形式で自動生成するスキル。 AI事業・IT事業・コンサルティング等に対応し、フリーランス新法（2024）・民法改正（2020）に準拠。 Anchors: - 契約書の作成実務と書式（牧野和夫）/ 適用: 契約構成・条項設計 / 目的: 実務レベルの契約書構造 - AIと著作権に関する考え方について（文化庁 令和6年）/ 適用: AI著作権条項 / 目的: AI利用免責設計 - フリーランスとして安心して働ける環境を整備するためのガイドライン（公取委・厚労省）/ 適用: 支払条件・解約予告 / 目的: 法令準拠 Trigger: 取引基本契約書, 業務委託契約, 契約書作成, フリーランス契約, AI事業契約, 請負契約, 準委任契約, 著作権譲渡契約

Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 with `bam_ip` + `bam_input` (control arm) and `bam_treated_ip` + `bam_treated_input` (treatment arm) for integrated GC-bias-aware differential calling (Liu 2022 *NAR Genom Bioinform* 4:lqac046), QNB beta-binomial test (Liu 2017 *BMC Bioinformatics* 18:387), MeTDiff HMM-based differential bundled with MeTPeak, RADAR (Zhang 2019 *Genome Biol* 20:294) with its `filterBins -> diffIP -> reportResult` workflow, and the defensible paired-symmetric case of edgeR / DESeq2 on featureCounts-on-peaks matrices when batch / lot covariates need explicit fixed-effect handling (exomePeak2's top-level API does NOT accept arbitrary covariates). Covers paired vs unpaired vs interaction designs, batch confounding (antibody lot, RNA prep, sequencing run) and the per-lot meta-analysis strategy when exomePeak2 is the primary caller, the stoichiometry-vs-expression-vs-IP-efficiency confound that all MeRIP differential methods inherit, normalisation choice (size factor on IP, on input, on per-sample IP/input ratio), the McIntyre 2020 reproducibility caveat, effect-size filtering as a guardrail against under-powered N=2 designs, and orthogonal-validation routes for absolute stoichiometry (GLORI / SAC-seq / m6Anet `mod_ratio`). Use when comparing m6A levels across two or more conditions, choosing between exomePeak2 / QNB / RADAR / MeTDiff for a given design, handling batch confounding when exomePeak2's API is too rigid, normalising against input properly, distinguishing real hyper- / hypo-methylation from expression-level shifts, applying effect-size thresholds, interpreting volcano plots of differential peaks, or planning a follow-up orthogonal stoichiometry validation.

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。

Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Nat Methods* 19:1590; multiple-instance-learning neural network over DRACH 5-mer signal). Covers the required upstream pipeline (Dorado / Guppy basecalling -> minimap2 transcriptome alignment with `-ax map-ont -uf -k14 --secondary=no` -> nanopolish eventalign with `--scale-events --signal-index` (m6Anet-required) plus `--summary` / `--threads` housekeeping -> m6anet dataprep -> m6anet inference), per-site vs per-read probability interpretation including the `mod_ratio` per-site stoichiometry column, the DRACH-only modeling constraint, minimum-coverage thresholds (20-50 reads per site for stable probability estimates), multi-condition comparison via xPore (Pratanwanich 2021 *Nat Biotechnol* 39:1394), Nanocompore (Leger 2021 *Nat Commun* 12:7198), ELIGOS (Jenjaroenpun 2021 *NAR* 49:e7), and Dorado native modification calling (RNA004 chemistry, 2024+), reference-transcriptome version pinning, the cDNA-vs-DRS chemistry distinction (cDNA-Nanopore CANNOT be used for modification detection), and orthogonal validation against MeRIP / GLORI. Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting per-site `probability_modified` vs `mod_ratio` vs per-read modification probabilities, comparing methylation between conditions from ONT data, deciding between m6Anet for known DRACH sites and Dorado/Remora for genome-wide screening, pinning RNA002 vs RNA004 chemistry and basecaller model versions, or troubleshooting eventalign / dataprep failures.

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 and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Cell Reports 36:109597), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen & Zwaenepoel 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DTL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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。

Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2020 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer 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。

Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 with `bam_ip` + `bam_input` (control arm) and `bam_treated_ip` + `bam_treated_input` (treatment arm) for integrated GC-bias-aware differential calling (Liu 2022 *NAR Genom Bioinform* 4:lqac046), QNB beta-binomial test (Liu 2017 *BMC Bioinformatics* 18:387), MeTDiff HMM-based differential bundled with MeTPeak, RADAR (Zhang 2019 *Genome Biol* 20:294) with its `filterBins -> diffIP -> reportResult` workflow, and the defensible paired-symmetric case of edgeR / DESeq2 on featureCounts-on-peaks matrices when batch / lot covariates need explicit fixed-effect handling (exomePeak2's top-level API does NOT accept arbitrary covariates). Covers paired vs unpaired vs interaction designs, batch confounding (antibody lot, RNA prep, sequencing run) and the per-lot meta-analysis strategy when exomePeak2 is the primary caller, the stoichiometry-vs-expression-vs-IP-efficiency confound that all MeRIP differential methods inherit, normalisation choice (size factor on IP, on input, on per-sample IP/input ratio), the McIntyre 2020 reproducibility caveat, effect-size filtering as a guardrail against under-powered N=2 designs, and orthogonal-validation routes for absolute stoichiometry (GLORI / SAC-seq / m6Anet `mod_ratio`). Use when comparing m6A levels across two or more conditions, choosing between exomePeak2 / QNB / RADAR / MeTDiff for a given design, handling batch confounding when exomePeak2's API is too rigid, normalising against input properly, distinguishing real hyper- / hypo-methylation from expression-level shifts, applying effect-size thresholds, interpreting volcano plots of differential peaks, or planning a follow-up orthogonal stoichiometry validation.

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。

Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Nat Methods* 19:1590; multiple-instance-learning neural network over DRACH 5-mer signal). Covers the required upstream pipeline (Dorado / Guppy basecalling -> minimap2 transcriptome alignment with `-ax map-ont -uf -k14 --secondary=no` -> nanopolish eventalign with `--scale-events --signal-index` (m6Anet-required) plus `--summary` / `--threads` housekeeping -> m6anet dataprep -> m6anet inference), per-site vs per-read probability interpretation including the `mod_ratio` per-site stoichiometry column, the DRACH-only modeling constraint, minimum-coverage thresholds (20-50 reads per site for stable probability estimates), multi-condition comparison via xPore (Pratanwanich 2021 *Nat Biotechnol* 39:1394), Nanocompore (Leger 2021 *Nat Commun* 12:7198), ELIGOS (Jenjaroenpun 2021 *NAR* 49:e7), and Dorado native modification calling (RNA004 chemistry, 2024+), reference-transcriptome version pinning, the cDNA-vs-DRS chemistry distinction (cDNA-Nanopore CANNOT be used for modification detection), and orthogonal validation against MeRIP / GLORI. Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting per-site `probability_modified` vs `mod_ratio` vs per-read modification probabilities, comparing methylation between conditions from ONT data, deciding between m6Anet for known DRACH sites and Dorado/Remora for genome-wide screening, pinning RNA002 vs RNA004 chemistry and basecaller model versions, or troubleshooting eventalign / dataprep failures.

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 and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Cell Reports 36:109597), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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。

Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen & Zwaenepoel 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DTL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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。

Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2020 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer 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。

External SSL VPN / remote-access appliance attack matrix — Cisco ASA/AnyConnect, Fortinet FortiGate/FortiOS, Citrix NetScaler/ADC, Palo Alto GlobalProtect, Pulse Secure / Ivanti Connect Secure, SonicWall, F5 Big-IP. Covers version fingerprinting, CVE matrix (2018-2026), AAA backend identification, default credentials, configuration-disclosure paths, pre-auth RCE/SSRF/path-traversal exploits where applicable. Built from authorized-engagement Cisco ASA testing plus 2024-2026 enterprise VPN CVE landscape. Use whenever the target's perimeter exposes any SSL VPN appliance or remote-access gateway — these are the most common initial-access points in 2024-2026 actor TTPs.

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Tests genotype-environment associations and identifies adaptive loci while correcting for the four-confound landscape (structure, demography, background selection, sampling design) using LFMM2 with mandatory K via sNMF cross-entropy elbow (LEA 3), BayPass Core/AUX/C2/IS with Omega covariance matrix, RDA / pRDA for polygenic adaptation (Forester 2018; requires imputed genotypes), OutFLANK with trimmed FST null, pcadapt, gradient forests (Ellis-Smith-Pitcher 2012, NOT mis-cited Ellis-Manel), Capblancq & Forester 2021 RDA Swiss-army-knife, genomic-offset prediction with Lind & Lotterhos 2025 three-regime caveat, Lotterhos-Whitlock sampling optima, Wang & Bradburd 2014 IBD vs IBE, and Circuitscape + ResistanceGA. Use when identifying adaptive loci across gradients, choosing K for LFMM2, deciding among GEA methods, predicting maladaptation with the novel-environment caveat, distinguishing IBD vs IBE, or optimizing sampling design.

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。

Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy framework, factor decomposition, genome-scale Perturb-seq (Replogle 2022 Cell, 2.5M cells), and per-perturbation single-cell DE. Use when running a single-cell CRISPR screen, choosing direct-capture vs CROP-seq architecture, filtering escaper cells, performing single-cell DE, integrating Perturb-seq with pathway analysis, scaling to GW CRISPRi via Replogle protocol, or analyzing multi-omics screens.

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。