File Ops
File manipulation and management
project-safety
by mseok
"Set up safety rules and folder structures for research projects. Prevent accidental data loss when Codex reorganizes files."
context-extraction
by crowdin
Writes meaningful ai_context values in Crowdin JSONL files for strings that need translator context. Use when extracting context, filling ai_context fields, adding context to ambiguous strings, or working with Crowdin JSONL context files.
ast-grep
by Kayunangka
Guide for writing ast-grep rules to perform structural code search and analysis. Use when users need to search codebases using Abstract Syntax Tree (AST) patterns, find specific code structures, or perform complex code queries that go beyond simple text search. This skill should be used when users ask to search for code patterns, find specific language constructs, or locate code with particular structural characteristics.
speccy
by slamb2k
Deep-dive interview skill for creating comprehensive specifications. Reviews existing code and docs, then interviews the user through multiple rounds of targeted questions covering technical implementation, UI/UX, concerns, and tradeoffs. Produces a structured spec via create-specification. Use when starting a new feature, system, or major change that needs a spec.
cve-reachability-analyzer
by ArabelaTso
Analyze CVE reachability in software repositories by examining how vulnerable dependencies are imported and used. Determines whether vulnerable components, classes, or functions are reachable from project code through call chain analysis, reflection detection, dynamic loading patterns, and configuration-gated behavior. Classifies each CVE as likely reachable, possibly reachable, or likely unreachable with supporting evidence. Use when analyzing security vulnerabilities in dependencies, performing post-disclosure CVE triage, assessing vulnerability impact, or when users ask to analyze CVE reachability, check if vulnerabilities are exploitable, or evaluate dependency security risks.
search
by brightdata
Search Google via Bright Data SERP API. Returns structured JSON results with title, link, and description. Requires BRIGHTDATA_API_KEY and BRIGHTDATA_UNLOCKER_ZONE environment variables.
file-manager
by RTGS2017
文件管理技能。用于创建、移动、复制、删除文件和文件夹，整理目录结构。当用户需要管理文件、整理文件夹或批量处理文件时使用。
symfony:symfony-cache
by MakFly
Implement resilient Symfony async workflows with idempotency, retries, and operational visibility. Use for symfony cache tasks.
migrate-nativewind-to-uniwind
by uni-stack
Migrate a React Native project from NativeWind to Uniwind. Use when the user wants to replace NativeWind with Uniwind, upgrade from NativeWind, switch to Uniwind, or mentions NativeWind-to-Uniwind migration. Handles package removal, config migration, Tailwind 4 upgrade, cssInterop removal, theme conversion, and all breaking changes.
anti-distill
by leilei926524-tech
"Anti-distillation for employee Skills. Clean your skill files — looks complete, but core knowledge removed. 反蒸馏：清洗你被迫写的 Skill 文件，看起来完整，但核心知识已被抽掉。"
bio-alignment-indexing
by GPTomics
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
bio-chipseq-qc
by GPTomics
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream analysis. Use when assessing ChIP-seq data quality metrics.
bio-differential-splicing
by GPTomics
Detects differential alternative splicing between conditions using rMATS-turbo (BAM-based) or SUPPA2 diffSplice (TPM-based). Reports events with FDR-corrected significance and delta PSI effect sizes. Use when comparing splicing patterns between treatment groups, tissues, or disease states.
bio-alignment-msa-parsing
by GPTomics
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. Use when parsing or manipulating multiple sequence alignments.
bio-molecular-io
by GPTomics
Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structure parsing, canonicalization, and full standardization pipeline including sanitization, normalization, and tautomer canonicalization. Use when loading chemical libraries, converting formats, or preparing molecules for analysis.
bio-reference-operations
by GPTomics
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.
bio-chipseq-motif-analysis
by GPTomics
De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.
packages-documentation
by reactive
Write, update, and format docs for public APIs - API reference, README, docstrings, usage examples, migration guides, deprecation notices
bio-sam-bam-basics
by GPTomics
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.
bio-alignment-filtering
by GPTomics
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
bio-alignment-io
by GPTomics
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
bio-atac-seq-atac-peak-calling
by GPTomics
Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.
bio-virtual-screening
by GPTomics
Performs structure-based virtual screening using AutoDock Vina 1.2 for molecular docking. Prepares receptor PDBQT files, generates ligand conformers, defines binding site boxes, and ranks compounds by predicted binding affinity. Use when screening chemical libraries against a protein structure to find potential binders.
bio-substructure-search
by GPTomics
Searches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore features, functional groups, or scaffold matches with atom mapping. Use when finding compounds containing specific chemical moieties or filtering libraries by structural features.