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Analyze repository structure and generate standardized AGENTS.md files that serve as contributor guides for AI agents. Measures LOC to determine character limits and produces 5-section documents covering overview, folder structure, patterns, conventions, and working agreements.
実装計画（implementation_plan.md）を日本語に翻訳し、モデル選定・リソース管理戦略を含めた正式な計画書として docs/developers/plans/ に保存する
A skill for writing and content creation
This skill should be used when the user asks about "output formatting", "concise responses", "Matt Pocock planning style", "scannable output", "action steps format", or needs guidance on communication and output formatting rules for Ralph agents.
Generates intuitive analogies to clarify complex technical concepts, aiding understanding for developers and non-technical audiences.
Creates compelling cliffhangers that enhance serialized content, building anticipation and engagement for future episodes.
This skill should be used when the user asks "what's wrong with this video", "why does this video look bad", "detect video artifacts", "find quality issues", "video has artifacts", "identify compression artifacts", or wants to diagnose specific quality problems in a video file.
Analyze video clips for quality issues, timing problems, and dialogue accuracy. Use when checking generated videos, validating clips, finding black frames, freeze frames, or audio sync issues.
音频关键字过滤工具 - 根据关键字配置自动识别并删除音频中的指定内容
Regression-check citation anchoring (citations stay in the same subsection) to prevent “polish drift” that breaks claim→evidence alignment. **Trigger**: citation anchoring, citation drift, regression, cite stability, 引用锚定, 引用漂移. **Use when**: after editing/polishing, you want to confirm citations...
Create new log articles in nibzard.com style. Use when the user says "write an article", "create a blog post", "new log entry", or mentions wanting to write about a topic, experience, or idea. This skill captures the established voice: conversational, narrative-driven, technically deep yet access...
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation differences between experimental conditions or cell types.
Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization. Use when starting IMC analysis from raw MCD files or preparing images for segmentation.
Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing. Use when analyzing spatial relationships between cell types, testing for neighborhood enrichment, or identifying cell-cell interaction patterns in imaging mass...
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.
Impute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, harmonizing data across genotyping platforms, or inferring variants not directly typed in array data.
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
Analyze transcription factor motif accessibility variability using chromVAR. Use when identifying which TF motifs show variable accessibility across samples or conditions in ATAC-seq data.
Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis. Use when combining screens from multiple batches or correcting systematic technical variation.
Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports.
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting exp...
Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps. Use when comparing Hi-C contacts between conditions.
Generate JSON API endpoints with authentication and versioning. Use when user needs API, mobile backend, external integration, or says "create API", "add endpoint", "JSON response", "API for mobile", "REST API".
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