「conversion」の検索結果

Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.

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Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using cooler (Python + CLI), hic2cool, and hictk. Covers the single-resolution mcool URI (file.mcool::/resolutions/<bp>), the load-bearing divisive-vs-multiplicative weight-naming rule (KR/VC/VC_SQRT auto-divisive vs cooler's multiplicative weight), what survives .hic<->.cool conversion (FRAG matrices and norm vectors do not), raw-vs-balanced coarsening, the .pairs upper-triangle/chromsize-order contract, and chrom-naming/bin-table provenance. Use when loading a cooler, converting .hic to .mcool, selecting a resolution, building a cooler from pairs or a matrix, coarsening/zoomifying, importing Juicer norm vectors, or debugging all-NaN balanced matrices and chr1-vs-1 empty fetches.

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Designs pegRNAs and nicking guides for prime editing (PE) -- choosing the nick/strand, tuning the primer-binding site (PBS) and reverse-transcription template (RTT) as a per-locus panel, selecting the PE system (PE2/PE3/PE3b/PE4/PE5/PEmax/PE7), adding MMR-evading and PAM-disrupting silent edits, appending epegRNA 3' motifs (tevopreQ1/mpknot), and ranking with PRIDICT/DeepPrime. Covers twinPE/PASTE for large insertions and the prime-vs-base-editing decision. Use when designing a scarless point mutation, small insertion/deletion, or any of the 12 base conversions without a double-strand break, when efficiency is low and MMR inhibition or pegRNA stabilization is needed, or when routing a large insertion to an integrase method. Generic guide scoring and base editing are separate skills.

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Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR (Python) implicit transpose, AnnData (cells-rows) <-> SingleCellExperiment (cells-cols) orientation flip, HDF5/h5ad vs Zarr cloud-native shift, HDF5SummarizedExperiment + DelayedArray for out-of-memory bulk, scanpy backed mode for large h5ad, the ~10-15% density crossover where dense beats sparse, 10X format proliferation (MTX vs CellRanger H5 vs h5ad), the dense-conversion memory blow-up, and Dask + Zarr for consortium-scale matrices. Use when choosing sparse format, working with single-cell-sized matrices, importing/exporting 10X, debugging R/Python interop transposes, processing matrices too large for RAM, or building cloud-native pipelines.

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces assembly_summary.txt scraping and many EFetch workflows). Use when bulk-pulling genome assemblies, gene metadata across species, ortholog sets, or BLAST databases; when E-utilities are too slow for genome-scale work; or when automatic checksum verification, parallel download, and clean accession-driven retrieval are required. Encodes the JSON-lines output format, dataformat conversion, --dehydrated for cloud workflows, and when Datasets is/isn't the right tool.

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Map N6-methyladenosine (m6A) RNA modifications at single-nucleotide resolution using miCLIP (Linder 2015), miCLIP2 + m6Aboost machine learning (Kortel 2021), GLORI (Liu 2023, antibody-free chemical conversion), DART-seq (Meyer 2019, APOBEC1-YTH fusion), m6Anet (nanopore direct RNA), or MeRIP-seq with calibration. Use when distinguishing antibody-based from antibody-free m6A detection methods, applying the DRACH motif constraint, reconciling cross-method disagreements (DART 44% in DRACH vs GLORI), or detecting m6Am at the cap.

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Generate SEO-optimized competitor comparison and alternatives pages. Covers "X vs Y" layouts, "alternatives to X" pages, feature matrices, schema markup, and conversion optimization. Use when user says "comparison page", "vs page", "alternatives page", "competitor comparison", "X vs Y", "versus", "compare competitors", or "alternative to".

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Image optimization analysis for SEO and performance. Checks alt text, file sizes, formats, responsive images, lazy loading, CLS prevention, image SERP rankings (via DataForSEO), and image file optimization (WebP/AVIF conversion, IPTC/XMP metadata injection). Use when user says "image optimization", "alt text", "image SEO", "image size", "image audit", "optimize images", "image metadata", "image SERP", "convert to webp", or "image file optimize".

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No-loss protocol for changing an existing mandate's output contract. Use when changing what an agent or mandate emits or how it is typed: binding a kind, declaring output_kind, kind-backfill batches, provision reconciliation, or any make-this-contract-honest sweep. NOT for creating a new agent (use create-agent).

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Adding a file type or upgrading any of its capability slots in the files feature (preview, edit, thumbnail, grid card, info, share, versions, conversion, diff, rail panel). Use when supporting a new extension or MIME type, building a previewer, touching FILE_TYPES, PreviewKind, FilePreview.tsx, EDITABLE_KINDS, or surfaces/single-file/, or working the FILE_SURFACES.md wishlist.

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Elite frontend image-direction skill for generating premium, conversion-aware website design references. CRITICAL OUTPUT RULE — generate ONE separate horizontal image FOR EVERY section. A landing page with 8 sections produces 8 images. Never compress multiple sections into one image. Enforces composition variety (not always left-text / right-image), background-image freedom, varied CTAs, varied hero scales (giant / mid / mini minimalist), narrative concept spine, second-read moments, and a single consistent palette across all images. Optimized for landing pages, marketing sites, and product comps that developers or coding models can accurately recreate.

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Calculate statistical significance for A/B tests. Sample size estimation, power analysis, and conversion rate comparisons with confidence intervals.

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Design and analyze A/B tests, calculate statistical significance, and determine sample sizes for conversion optimization and experiment validation

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The science of learning through controlled experimentation. A/B testing isn't about picking winners—it's about building a culture of validated learning and reducing the cost of being wrong. This skill covers experiment design, statistical rigor, feature flagging, analysis, and building experimentation into product development. The best experimenters know that every test, positive or negative, teaches something valuable. Use when "a/b test, experiment, hypothesis, statistical significance, sample size, feature flag, variant, control, treatment, p-value, conversion rate, test winner, split test, experimentation, testing, statistics, feature-flags, hypothesis, growth, optimization, learning, validation" mentioned.

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Master AngularJS to Angular migration, including hybrid apps, component conversion, dependency injection changes, and routing migration.

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Production pipeline for ASCII art video — any format. Converts video/audio/images/generative input into colored ASCII character video output (MP4, GIF, image sequence). Covers: video-to-ASCII conversion, audio-reactive music visualizers, generative ASCII art animations, hybrid video+audio reactive, text/lyrics overlays, real-time terminal rendering. Use when users request: ASCII video, text art video, terminal-style video, character art animation, retro text visualization, audio visualizer in ASCII, converting video to ASCII art, matrix-style effects, or any animated ASCII output.

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Generates a Python CLI tool for bidirectional conversion between 4-byte floating-point numbers and hexadecimal memory representations, featuring a continuous loop and robust input parsing.

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Converts X (Twitter) tweets and articles to markdown with YAML front matter. Uses reverse-engineered API requiring user consent. Use when user mentions "X to markdown", "tweet to markdown", "save tweet", or provides x.com/twitter.com URLs for conversion.

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Complete color manipulation and green screen effects system. PROACTIVELY activate for: (1) Green screen/chromakey removal, (2) Color grading with LUTs, (3) Color correction (levels, curves, white balance), (4) Colorkey/color removal effects, (5) Hue/saturation manipulation, (6) Color space conversions (BT.709, BT.2020, HDR), (7) Color isolation effects, (8) Teal and orange look, (9) Vintage/film looks, (10) Color keying for transparency. Provides: chromakey and colorkey filters, LUT application (lut3d), curves and levels adjustment, color balance, selective color manipulation, color space handling, HDR tone mapping, professional color grading chains.

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Design, audit, and improve analytics tracking systems that produce reliable, decision-ready data. Use when the user wants to set up, fix, or evaluate analytics tracking (GA4, GTM, product analytics, events, conversions, UTMs). Focuses on measurement strategy, signal quality, and validation — not just firing events.

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Complete marketing strategy for Shopify stores. SEO, email marketing, paid ads, social media, conversion optimization, and retention tactics specifically tailored for Shopify/DTC brands.

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World-class autonomous sales and revenue skill system. Use ANY time the user asks to sell, pitch, prospect, close, negotiate, launch, monetize, build funnels, write outreach, craft proposals, develop pricing, design offers, write sales copy, create email sequences, plan campaigns, position products, handle objections, create playbooks, build pipeline, forecast revenue, develop GTM strategy, optimize conversions, write ad copy, create sales decks, score leads, nurture prospects, upsell, cross-sell, retain customers, write case studies, price products, structure enterprise deals, create battle cards, script discovery calls, build affiliate programs, plan product launches, create webinar funnels, design pricing pages, A/B test offers, analyze unit economics, calculate LTV/CAC, or ANY other sales, revenue, monetization, go-to-market, or commercial growth task. If it involves selling, revenue, deals, pipeline, or commercial strategy — USE THIS SKILL. Trigger aggressively.

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Query Google Analytics 4 (GA4) data via the Analytics Data API. Use when you need to pull website analytics like top pages, traffic sources, user counts, sessions, conversions, or any GA4 metrics/dimensions. Supports custom date ranges and filtering.

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