2,371 skills found · Page 73 of 80
jaechang-hits / bakta-genome-annotationAnnotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT, and gaps against a curated UniRef-derived database.
jaechang-hits / prokka-genome-annotationAnnotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA, tmRNA, signal peptides against Pfam, TIGRFAMs, RefSeq. Outputs GFF3, GenBank, FASTA, TSV. Use PGAP for NCBI GenBank submission; Bakta for faster NCBI-compatible annotation.
jaechang-hits / roary-pangenomeCompute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline. Builds gene presence/absence matrices, core/soft-core/shell/cloud partitions, multi-FASTA core gene alignments (with `-e`), and a pan-genome reference.
jaechang-hits / bioservices-multi-databaseUnified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI.
jaechang-hits / busco-status-interpretationGuide to interpreting BUSCO completeness statuses: why Duplicated BUSCOs count as complete, parsing output files, computing/comparing completeness across proteomes/genomes, common counting mistakes
jaechang-hits / fastp-fastq-preprocessingAll-in-one FASTQ QC and adapter trimming. Auto-detects Illumina adapters, filters low-quality reads, corrects paired-end overlaps, emits HTML+JSON QC in one pass. 3-10x faster than Trim Galore/Trimmomatic. First step before STAR, BWA-MEM2, or Salmon.
jaechang-hits / celltypist-cell-annotationAutomated scRNA-seq cell type annotation via pre-trained logistic regression. 45+ models: immune, gut, lung, brain, fetal, cancer microenvironments. Input normalized AnnData; outputs per-cell labels, majority-vote cluster labels, confidence scores.
jaechang-hits / cellxgene-censusQuery CELLxGENE Census (61M+ cells). Search by cell type/tissue/disease/organism; get AnnData, stream out-of-core, train PyTorch models. For your own data use scanpy; for annotated data use anndata.
jaechang-hits / scanpy-scrna-seqscRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference. Standard scRNA-seq exploration.
jaechang-hits / pathmlComputational pathology toolkit for whole-slide images (WSIs): load slides, extract tiles, stain normalization, nuclear segmentation, feature extraction, and ML training. Supports H&E and multiplex. For end-to-end pipelines from raw WSIs to quantitative outputs.
jaechang-hits / multiqc-qc-reportsAggregates QC from 150+ bioinformatics tools into one interactive HTML report. Scans FastQC, samtools, STAR, HISAT2, Trim Galore, featureCounts, Kallisto, Salmon, Picard, GATK logs; merges per-sample stats with plots. For NGS pipeline-wide QC.
jaechang-hits / sciagent-skill-creatorScaffold a new SciAgent-Skills entry. Picks pipeline/toolkit/database/guide template, creates skills/{category}/{name}/SKILL.md with valid frontmatter, appends the registry.yaml entry, runs validation. Enforces name uniqueness, kebab-case, description keyword rules, schema rules from AGENTS.md.
jaechang-hits / exploratory-data-analysisMethodology for exploratory data analysis on scientific files. Decision frameworks by data type (tabular, sequence, image, spectral, structural, omics), quality assessment, report generation, format detection across 200+ formats
jaechang-hits / citation-managementSelecting a reference manager and applying citation styles. Compares Zotero, Mendeley, EndNote, Paperpile; covers APA/Vancouver/ACS/Nature styles, DOI management, citation tracking, and Word/Google Docs/LaTeX integration
jaechang-hits / scientific-schematicsDesigning scientific schematics, diagrams, and graphical abstracts. Covers tool selection (BioRender, Inkscape, Affinity, PowerPoint), design principles for pathway diagrams, mechanism schematics, experimental workflows, and journal graphical abstracts.
jaechang-hits / general-figure-guideUniversal QA checklist for generated scientific plots: overlapping labels, clipped text, missing axes/legends, overcrowded data, and cross-journal resolution/format guidance.
jaechang-hits / hypothesis-generationStructured hypothesis formulation: turn observations into testable hypotheses with predictions, propose mechanisms, design experiments. Follows the scientific method. Use scientific-brainstorming for open ideation; hypogenic for automated LLM hypothesis testing on datasets.
giuseppe-trisciuoglio / developer-kitModular plugin marketplace for Claude Code and agentic CLIs, with validated, spec-driven skills, agents, commands, and workflows for Java, TypeScript, Python, PHP, AWS, and AI.
giuseppe-trisciuoglio / langchain4j-rag-implementation-patternsProvides Retrieval-Augmented Generation (RAG) implementation patterns with LangChain4j for Java. Generates document ingestion pipelines, embedding stores, vector search, and semantic search capabilities
giuseppe-trisciuoglio / codexProvides Codex CLI delegation workflows for complex code generation and development tasks using OpenAI's GPT-5.3-codex models, including English prompt formulation, execution flags, sandbox modes, and safe result handling
giuseppe-trisciuoglio / sonarqube-mcpProvides SonarQube and SonarCloud integration patterns via the Model Context Protocol (MCP) server. Enables quality gate monitoring, issue discovery and triaging, pre-push code analysis, and rule education directly in the agent workflow
giuseppe-trisciuoglio / aws-cloudformation-bedrockProvides AWS CloudFormation patterns for Amazon Bedrock resources including agents, knowledge bases, data sources, guardrails, prompts, flows, and inference profiles
giuseppe-trisciuoglio / aws-cloudformation-lambdaProvides AWS CloudFormation patterns for Lambda functions, layers, API Gateway integration, event sources, cold start optimization, monitoring, logging, template validation, and deployment workflows
giuseppe-trisciuoglio / prompt-engineeringProvides workflows to write, debug, and optimize prompts for LLMs, including few-shot example selection, chain-of-thought structuring, system prompt design, and template composition
giuseppe-trisciuoglio / ragImplements document chunking, embedding generation, vector storage, and retrieval pipelines for Retrieval-Augmented Generation systems
giuseppe-trisciuoglio / docs-updaterProvides automated documentation updates by analyzing git changes between the current branch and the last release tag. Performs git diff analysis to identify modifications, then updates README.md, CHANGELOG.md following Keep a Changelog standard, and discovers documentation folders for contextual up…
giuseppe-trisciuoglio / langchain4j-spring-boot-integrationProvides integration patterns for LangChain4j with Spring Boot. Configures AI model beans, sets up chat memory with Spring context, integrates RAG pipelines with Spring Data, and handles auto-configuration, dependency injection, and Spring ecosystem integration
giuseppe-trisciuoglio / langchain4j-testing-strategiesProvides unit test, integration test, and mock AI patterns for LangChain4j applications. Creates mock LLM responses, tests retrieval chains, validates RAG workflows, and implements Testcontainers-based integration tests for Java AI services
giuseppe-trisciuoglio / spring-boot-crud-patternsProvides and generates complete CRUD workflows for Spring Boot 3 services. Creates feature-focused architecture with Spring Data JPA aggregates, repositories, DTOs, controllers, and REST APIs. Validates domain invariants and transaction boundaries
giuseppe-trisciuoglio / geminiProvides Gemini CLI delegation workflows for large-context analysis and complex reasoning using Gemini 3.0 Flash and Gemini 3.0 Pro models, including English prompt formulation, execution flags, and safe result handling
