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Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution. Use when building portable pipelines with container support, running workflows on...
Decision rules for when to use MCP Qdrant-Indexer semantic search vs grep/literal file tools. Use this skill when starting exploration, debugging, or answering "where/why" questions about code.
Codebase search and context retrieval for any programming language. Hybrid semantic/lexical search with neural reranking. Use for code lookup, finding implementations, understanding codebases, Q&A grounded in s...
Provides comprehensive technical analysis for stocks and ETFs using RSI, MACD, Bollinger Bands, and other indicators. Activates when user requests stock analysis, technical indicators, trading signals, or marke...
配图助手 - 把文章/模块内容转成统一风格、少字高可读的 16:9 信息图提示词；先定“需要几张图+每张讲什么”，再压缩文案与隐喻，最后输出可直接复制的生图提示词并迭代。
Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution platforms, sharing pipelines with collab...
Search enterprise context data (Slack, docs, meetings, PRs) from the HERB benchmark to answer questions about products, employees, customers, and organizational activities. Use when answering questions that req...
Write revdep/issue.md to group packages by common error categories
Read and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration. Use when loading and inspecting flow or mass cytometry data before preprocessing.
Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Uses a ranked gene list to find coordinated changes in gene sets without requiring arbitrary significance cutoffs. Detects subtle but coordi...
Transcribe DNA to RNA and translate to protein using Biopython. Use when converting between DNA, RNA, and protein sequences, finding ORFs, or using alternative codon tables.
Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis.
Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLINK, scikit-allel, and LDBlockShow.
Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant proteinGroups.txt. Handles common preprocessing steps like contaminant filtering and missing va...
WikiPathways enrichment using clusterProfiler and rWikiPathways. Performs over-representation analysis and GSEA on community-curated biological pathways. WikiPathways is an open, collaborative platform with pat...
Compute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial autocorrelation, co-occurrence analysis, and neighborhood enrichment.
Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use for fast, accurate transcript-level quantification directly from FASTQ files without genome alignment.
Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology analysis. Use when interpreting metabolomics results in the context of biochemical pathway...
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use for whole genome sequencing, exome sequencing, and ChIP-seq alignment.
Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants. Use when characterizing resistance profiles in clinical isolates, sur...
Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating Seurat objects and AnnData objects, and...
Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold cha...
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use for comparing alignment quality, measuring sequence divergence, and analyzing...
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for running PCA, computing neighbors, clustering with Leiden/Louvain algorithms, generating UMAP/tSNE em...
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