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Prepare audio stems, the separate parts of a track, for mixing by matching their durations with silence, loops, or crossfades. Verify each generated and processed file before moving to the next production step.
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Plan or run bulk RNA-seq processing from sequencing reads to count matrices, tables of expression counts across samples. Check sample metadata, reference consistency, read mapping, and quantification quality, and produce summaries for downstream analysis.
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Create 2D sprite animations from an approved character frame. Generate all frames together, normalize their size and alignment, and prepare preview sheets to check consistency before using the animation in a game.
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Edits existing Canva designs by revising or translating text, replacing images and videos, adjusting text formatting, and moving or resizing elements. Presents a preview and change summary before saving approved edits to the design.
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Review a functionally complete interface before release and fix details in spacing, alignment, typography, wording, and interaction states. The skill also covers responsive layouts, accessibility, loading behavior, and code cleanup as part of the final quality pass.
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Improve interface layouts by reviewing spacing, alignment, content density, and visual hierarchy, the cues that show what matters most. Refine repetitive card grids and crowded sections into compositions with consistent spacing and responsive structure.
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Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM. Use for homolog search, UniRef30/ColabFold env searches, A3M or FASTA alignments, paired MSA search for complexes, PDB70 structural templates, hosted NVIDIA API calls, or local Docker deployment. For local deployment, download the databases in parallel with aria2c and launch via NIM_MODEL_NAME (the recommended default fast path, ~14 min vs over 80 min for the built-in downloader); a plain docker run uses the slow built-in downloader.
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[omh] Repository vocabulary unclear or inconsistent: project terminology alignment workflow: look up, capture, correct, and align the words a repository uses before planning or handoff. Use when the user says: ulw-context, project terminology alignment, review project terms, align project terminology, terminology this project uses.
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Performs multiple sequence alignment of proteins with EBI Clustal Omega. Use when you need to align multiple sequences to assess similarity, domain conservation, or key residue conservation. Supports up to 4000 sequences and a maximum file size of 4 MB. Do not use to search for homologous proteins in a database (use MMseqs2, BLAST), align non-protein sequences (DNA, RNA), perform structural alignment (use Foldseek, PyMOL), or if you only have a single sequence.
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Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.
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Build alignment artifacts — responsibility matrices, decision rights, and communication plans. Use when unclear ownership stalls decisions. For persuading in the moment, use `design-negotiation` (designer-toolkit).
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Review code changes for bugs and alignment with OpenEnv principles and RFCs. Use when reviewing PRs, checking code before commit, or when asked to review changes. Implements two-tier review model.
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Use when designing or auditing AAAI experiments for the broad-AI program committee, including baselines, ablations, statistical significance, robustness, human evaluation, AI-for-Social-Impact and alignment/safety evidence, compute and cost reporting, and reproducibility-checklist alignment for Phase-1 survival.
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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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Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.
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Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.
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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.
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Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.
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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.
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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.
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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.
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When the user wants to plan paid ads strategy, allocate ad budget, or choose paid channels. Also use when the user mentions "paid ads," "paid media," "PPC," "SEM," "web ads," "app ads," "TV ads," "CTV," "OOH," "banner ads," "ad network," "ad alliance," "Taaft ads," "Shopify App Store ads," "Google Ads," "Meta Ads," "PMF testing," "PMF validation," "test product-market fit with ads," "ad spend," "ad budget," "ROAS," "paid acquisition," "Quality Score," or "ad-to-page alignment." For Google Ads execution, use google-ads. For Meta Ads execution, use meta-ads. For landing page alignment, use landing-page-generator.
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Cascades strategy from boardroom to individual contributor and detects misalignment. Use when teams pull in different directions, OKRs don't connect, departments optimize locally at company expense, or strategy doesn't translate to execution.
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Compares two or more band-tagged frameworks and produces a framework-neutral topic matrix showing coverage and gaps across all inputs, plus an optional reference-centric PLC crosswalk document when a reference framework is supplied.
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