3,611 skills found · Page 108 of 121
jaechang-hits / mofaplus-multi-omicsMulti-Omics Factor Analysis v2 (MOFA+) with mofapy2. Jointly decompose omics layers (scRNA, ATAC, proteomics, methylation) into latent factors capturing major variation. Multi-group designs.
jaechang-hits / samtools-bam-processingCLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.
jaechang-hits / ucsc-genome-browserQuery UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies. Retrieve sequence by region, list/fetch BED/bigWig tracks, chromosome sizes, RefSeq/GENCODE gene structures, PhyloP/PhastCons scores.
jaechang-hits / bedtools-genomic-intervalsGenomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest features. Core for ChIP-seq peak annotation, region filtering, genome arithmetic. Use tabix for indexed single-region queries; use deeptools for normalized bigWig coverage.
jaechang-hits / gtarsRust-backed Python library for fast genomic token arithmetic and BED processing. High-performance BED I/O, interval set ops (intersect, merge, complement, subtract), region tokenization against a universe, universe construction. Use for preprocessing large BED collections and ML token vocabularies.
jaechang-hits / deseq2-differential-expressionBulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for Python; use edgeR for TMM normalization.
jaechang-hits / popv-cell-annotationConsensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via majority voting. Outputs per-method labels, consensus, agreement score
jaechang-hits / statistical-significance-annotationGuide for annotating statistical significance (p-value asterisks) on comparison plots. Covers standard notation (ns, *, **, ***, ****), matplotlib bracket+asterisk implementation, and use with seaborn box/violin/bar plots
jaechang-hits / nan-safe-correlationPer-feature NaN-safe Spearman/Pearson correlation across many features (genes, proteins, variants) with missing values. Covers why bulk matrix shortcuts fail, correct pairwise deletion, degenerate input filtering, and large-dataset performance.
jaechang-hits / lancet-figure-guideThe Lancet figure preparation: resolution (300+ DPI at 120%), preferred editable formats (PowerPoint/Word/SVG), column widths (75/154 mm), Times New Roman, in-house redraw policy.
jaechang-hits / kegg-pathway-analysisGuide to KEGG pathway enrichment for DEG results. Covers ORA vs GSEA, mandatory directionality splitting, KEGG organism codes, API failure handling with offline fallbacks, cross-condition comparisons, and answer-first reporting. Consult when running enrichment with clusterProfiler or gseapy.
jaechang-hits / statistical-analysisGuided statistical analysis: test choice, assumption checks, effect sizes, power, APA reporting. Pick tests, verify assumptions, or format results for publication. Covers frequentist (t-test, ANOVA, chi-square, regression, correlation, survival, count, reliability) and Bayesian.
jaechang-hits / scientific-visualizationGuide for choosing and creating scientific visualizations for publications and talks. Covers chart-type selection by data structure, color theory for accessibility/print, figure composition, journal formatting (Nature, Cell, ACS), and common pitfalls.
jaechang-hits / sar-analysisStructure-activity relationship (SAR) analysis guide for drug discovery including molecular descriptor analysis, scaffold analysis, and activity cliff detection.
jaechang-hits / depmap-crispr-essentialityDepMap CRISPR gene effect (Chronos) analysis: sign convention for essentiality, per-gene NaN-safe Spearman correlation, data loading/alignment. For general NaN-safe correlation see nan-safe-correlation; for quality filtering see degenerate-input-filtering.
kazukinagata / e-taxThis skill should be used when the user wants to file their tax return electronically via the 確定申告書等作成コーナー (NTA Tax Return Preparation Corner) using Claude in Chrome, Antigravity Browser Sub-Agent, or Playwright CLI (fallback). It guides the browser-based input of calculated tax data.
kazukinagata / income-taxThis skill should be used when the user needs to calculate their income tax (所得税), compute deductions, or import withholding slips. Trigger phrases include: "所得税を計算", "確定申告書を作成", "控除を計算", "源泉徴収票を取り込む", "所得税額", "納付額を計算", "還付額を計算", "第一表", "第二表", "申告書B", "所得控除", "税額控除".
kazukinagata / assessThis skill should be used when the user asks to determine what tax filings they need, wants to know if they must file a tax return (確定申告), asks about consumption tax obligations (消費税), or needs help understanding their filing requirements.
kazukinagata / consumption-taxThis skill should be used when the user needs to calculate consumption tax (消費税) or determine their tax method (2割特例, 簡易課税, or 本則課税). Trigger phrases include: "消費税を計算", "消費税の申告", "消費税申告書", "2割特例", "簡易課税", "本則課税", "課税売上", "消費税額", "インボイス", "みなし仕入率", "課税仕入".
kazukinagata / settlementThis skill should be used when the user needs to perform year-end closing adjustments (決算整理), review financial statements (決算書), compute depreciation, or review their trial balance.
kazukinagata / setupThis skill should be used when the user wants to set up shinkoku for the first time, initialize their configuration, or update their existing settings. Trigger phrases include: "セットアップ", "初期設定", "設定ファイルを作る", "shinkokuの設定", "config", "setup", "始め方", "使い方", "設定を更新", "configを作り直す".
kazukinagata / submitThis skill should be used when the user is ready to submit their tax return, needs a final review checklist, wants to know how to submit (e-Tax, mail, or in-person), or asks about common mistakes before submission.
kazukinagata / incorporation法人成り（個人事業主から法人への移行）に関する相談。税額比較シミュレーション、 法人形態の選択、設立手続き、役員報酬戦略、社会保険の比較を支援する。 Trigger: "法人成り", "会社設立", "法人化", "株式会社にしたい", "合同会社", "法人税と所得税の比較", "役員報酬", "法人成りのタイミング", "マイクロ法人", "1人法人"
kazukinagata / tax-advisorThis skill should be used when the user asks tax-related questions, wants advice on deductions or tax savings, or needs expert guidance equivalent to a tax accountant (税理士) or life planner.
giuseppe-trisciuoglio / drawio-logical-diagramsCreates professional logical flow diagrams and logical system architecture diagrams using draw.io XML format (.drawio files)
giuseppe-trisciuoglio / clean-architectureProvides implementation patterns for Clean Architecture, Hexagonal Architecture (Ports & Adapters), and Domain-Driven Design in Java 21+ Spring Boot 3.5+ applications
giuseppe-trisciuoglio / aws-drawio-architecture-diagramsCreates professional AWS architecture diagrams in draw.io XML format (.drawio files) using official AWS Architecture Icons (aws4 library)
giuseppe-trisciuoglio / spring-ai-mcp-server-patternsProvides Spring Boot MCP server patterns that create Model Context Protocol servers with Spring AI by defining tool handlers, exposing resources, configuring prompt templates, and setting up transports for AI function calling and tool calling
giuseppe-trisciuoglio / unit-test-cachingProvides patterns for unit testing Spring Cache annotations (@Cacheable, @CachePut, @CacheEvict). Generates test code that mocks cache managers, verifies cache hit/miss behavior, tests cache key generation with SpEL expressions, validates eviction strategies, and checks conditional caching scenarios…
giuseppe-trisciuoglio / unit-test-config-propertiesProvides patterns for unit testing `@ConfigurationProperties` classes with `@ConfigurationPropertiesTest`. Validates property binding, tests validation constraints, verifies default values, checks type conversions, and mocks property sources for Spring Boot configuration properties
