File Ops
File manipulation and management
artifacts-builder
by Kilo-Org
Suite of tools for creating elaborate, multi-component HTML artifacts using modern frontend web technologies (React, Tailwind CSS, shadcn/ui). Use for complex artifacts requiring state management, routing, or shadcn/ui components - not for simple single-file HTML/JSX artifacts.
delaware-franchise-tax
by open-agreements
File your Delaware annual franchise tax and annual report. Guides you through tax calculation (Authorized Shares and Assumed Par Value Capital methods), the eCorp portal filing process, and payment. For Delaware C-Corps (March 1 deadline) and LLCs/LPs/GPs (June 1 deadline).
falcon-strategy
by Senpi-ai
FALCON v1.0.0 — Conversion-Event Momentum (XYZ Pre-IPO → equity). A Pre-IPO Perpetual (IPOP) carries a structural funding signature ( funding <= ~1e-7, max_leverage <= 5) and is price-throttled by trade.xyz Discovery Bounds. When the company IPOs the product CONVERTS to a standard equity perp — funding jumps ~100x, the leverage cap lifts, the throttle is removed — opening free price discovery. Falcon detects the IPOP→STANDARD flip and trades the post-conversion momentum. Distinct from Lemur, which trades the IPOP basket while it is still an IPOP. Wide let-winners-run DSL, 7d hard_timeout.
hydra-strategy
by Senpi-ai
HYDRA v2.0 — Single-Coin Conviction Fund with a CROSS-ASSET hedge. A long-term conviction book on ONE major (the thesis), cushioned by a diversified short of OTHER assets. ONE producer, parameterized by HYDRA_COIN + HYDRA_LEG (core dip hedge). CORE rides the coin's trend as a LONG-TERM HOLD on a catastrophic-only DSL (you don't get shaken out on normal volatility). DIP buys pullbacks within a confirmed uptrend (tactical add). HEDGE (v2.0) shorts a diversified BLEND of OTHER assets that are actually breaking down — vol-parity sized, scaled up when the thesis coin is itself breaking — so it cushions market risk WITHOUT betting against the thesis. Never shorts the thesis coin. Deploy for ETH, SOL, HYPE (or any major) = three wallets each. NOT a copy-trader; the runtime owns the LLM gate (pass-through), DSL exits, and all risk.guard_rails.
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.
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.
bio-causal-genomics-fine-mapping
by GPTomics
Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. Computes posterior inclusion probabilities and credible sets to prioritize variants for functional follow-up. Use when narrowing GWAS association signals to candidate causal variants or building credible sets for functional validation.
Workspace Health Check Skill
by jmagly
/check-traceability - Verify requirement links
vue
by nuxt-content
Use when editing .vue files, creating Vue 3 components, writing composables, or testing Vue code - provides Composition API patterns, props/emits best practices, VueUse integration, and reactive destructuring guidance
make
by mohitmishra786
GNU Make skill for C/C++ build systems. Use when writing or debugging Makefiles, understanding pattern rules and automatic dependency generation, managing CFLAGS/LDFLAGS, converting ad-hoc compile commands into maintainable Makefiles, or diagnosing incremental build issues. Activates on queries about Makefiles, make targets, pattern rules, phony targets, dependency tracking, recursive make, or make errors.
shellck
by regenrek
Run shellcheck on shell scripts after editing scripts or when debugging shell errors. Use for linting scripts in a repo (especially scripts/), catching issues like set -u with unset vars, bad subshell usage, or quoting mistakes.
Bun Bundler
by secondsky
This skill should be used when the user asks about "bun build", "Bun.build", "bundling with Bun", "code splitting", "tree shaking", "minification", "sourcemaps", "bundle optimization", "esbuild alternative", "building for production", "bundling TypeScript", "bundling for browser", "bundling for Node", or JavaScript/TypeScript bundling with Bun.
Bun TanStack Start
by secondsky
TanStack Start full-stack React framework with Bun runtime. Use for TanStack Router, server functions, vinxi, or encountering SSR, build, preset errors.