CLI Tools
Command line utilities
hackage-release
by colonelpanic8
Use when user asks to release, publish, or bump version of a Haskell package to Hackage
file-manager
by openakita
文件和目录管理工具。创建、读取、写入、删除、移动、复制文件。 搜索文件、列出目录、获取文件信息。 关键词: 文件, 目录, 创建, 删除, 复制, 移动, 搜索, 列出
datetime-tool
by openakita
获取当前时间、格式化日期、计算日期差值、时区转换。 当用户询问时间、日期、时区相关问题时使用此技能。 关键词: 时间, 日期, 时区, 今天, 现在, 星期, 几点
webapp-testing
by openakita
Toolkit for interacting with and testing local web applications using Playwright. Supports verifying frontend functionality, debugging UI behavior, capturing browser screenshots, and viewing browser logs.
uv-pip-install
by Memento-Teams
Install and manage Python packages using uv pip. Use when a Python import fails with ModuleNotFoundError, user asks to install a package, or a script requires a missing dependency.
vue
by antfu
Vue 3 Composition API, script setup macros, reactivity system, and built-in components. Use when writing Vue SFCs, defineProps/defineEmits/defineModel, watchers, or using Transition/Teleport/Suspense/KeepAlive.
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.
data-privacy-agreement
by open-agreements
Draft and fill data privacy agreement templates — DPA, data processing agreement, GDPR, HIPAA BAA, business associate agreement, AI addendum. Produces signable DOCX files from Common Paper standard forms.
employment-contract
by open-agreements
Draft and fill employment agreement templates — offer letter, IP assignment, PIIA, confidentiality acknowledgement. Produces signable DOCX files from OpenAgreements standard forms for hiring employees.
safe
by open-agreements
Draft and fill Y Combinator SAFE templates — valuation cap, discount, MFN, pro rata side letter. Standard startup fundraising documents for convertible equity. Produces signable DOCX files.
services-agreement
by open-agreements
Draft and fill services agreement templates — consulting contract, contractor agreement, SOW, statement of work, professional services agreement. Produces signable DOCX files from Common Paper and Bonterms standard forms.
ospec
by clawplays
Document-driven OSpec workflow for AI-assisted development with change-ready initialization, execution, validation, and archive readiness.
bio-chipseq-visualization
by GPTomics
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions. Use when visualizing ChIP-seq signal and peaks.
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-atac-seq-nucleosome-positioning
by GPTomics
Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. Use when analyzing chromatin organization, identifying nucleosome-free regions at promoters, or characterizing nucleosome occupancy patterns from ATAC-seq fragment size distributions.
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-atac-seq-footprinting
by GPTomics
Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identifying TF occupancy patterns within accessible regions, as TF binding protects DNA from Tn5 cutting.
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-atac-seq-atac-qc
by GPTomics
Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity. Use when assessing ATAC-seq library quality before or after peak calling to identify problematic samples.
bio-splicing-quantification
by GPTomics
Quantifies alternative splicing events (PSI/percent spliced in) from RNA-seq using SUPPA2 from transcript TPM or rMATS-turbo from BAM files. Calculates inclusion levels for skipped exons, alternative splice sites, mutually exclusive exons, and retained introns. Use when measuring splice site usage or isoform ratios from RNA-seq data.
bio-pileup-generation
by GPTomics
Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.
bio-alignment-validation
by GPTomics
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.
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.