51 skills · sorted by relevance
Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization, and signal processing. Use when handling coverage and signal tracks from ChIP-seq, ATAC-seq, or RNA-seq.
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EEG preprocessing and analysis — filtering, artifact removal, time-frequency decomposition, and ERP workflows.
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Execute CUT&RUN processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing CUT&RUN or CUT&Tag data, an alternative to ChIP-seq with lower background. Trigger on: CUT&RUN pipeline, CUT&Tag, SEACR, Henikoff, targeted chromatin, pA-MNase, process CUT&RUN.
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Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing RNA-seq data with STAR alignment, RSEM/Kallisto quantification, or generating expression matrices. Trigger on: RNA-seq pipeline, gene expression, STAR alignment, RSEM quantification, transcript quantification, TPM, FPKM, RNA processing, run RNA-seq.
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Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.
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Frequency-domain analysis — FFT, power spectral density (Welch/periodogram), spectrograms, wavelet transforms, and coherence. Use for any signal with periodic, quasi-periodic, or transient frequency content in physics data.
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Summarize customer interview transcripts into a consistent Markdown document. Capture what customers want to accomplish, their current solutions, satisfaction and problems, notable findings, and follow-up actions with dates and owners when available.
Investigate file inclusion and path traversal flaws that let applications access unintended files. The skill guides checks for sensitive data exposure and possible code execution, using content evidence or repeatable indirect signals to avoid false positives.
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Guppy is deprecated; use Dorado for all new analyses.
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Specify algorithms for Model-Based Design: system specs, architecture specs, implementation plans, test plans. Use when creating specifications for controllers, signal processing, diagnostics, estimators, or other algorithms authored in Simulink, Stateflow, System Composer, or MATLAB Function blocks.
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Use when designing a Digital Down Converter (DDC) using dsphdl System objects. Triggers on requests involving DDC design, frequency down-conversion for FPGA/ASIC, NCO + mixer + decimation filter chains, fractional/non-integer sample rate conversion, or HDL-optimized receiver front-end signal processing.
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MATLAB-style numerical computing, matrix operations, and signal processing
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Neurophysiological signal processing for ECG, EEG, EMG, and more
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Draft, restructure, and diagnose IEEE-style technical manuscript sections using a routed static/dynamic workflow. Use for IEEE conference, journal, Transactions, Letters, or magazine papers when writing titles, abstracts, introductions, related work, methods, experiments, conclusions, contribution statements, section outlines, or Chinese-to-English engineering paper drafts in AI, computer science, communications, control, signal processing, electrical/electronic engineering, power, robotics, circuits, and applied systems.
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MATLAB/GNU Octave numerical computing: matrices, linear algebra, ODEs, signal processing, optimization, statistics, scientific visualization. MATLAB-syntax examples run on both. For Python use numpy/scipy; for statistical modeling use statsmodels.
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Apply the bioengineering, translational systems biology, and tissue modeling frameworks of Linda Griffith, Professor of Biological Engineering at MIT and tissue engineering pioneer. Use this skill whenever facing decisions, designs, or evaluations in bioengineering, tissue modeling, microphysiological systems (organs-on-chips), synthetic matrix design, disease subtyping, or drug target validation. Reach for this skill when evaluating preclinical models (human vs. animal), reframing overlooked or neglected pathologies into rigorous engineering challenges, selecting biomaterials, designing cell signal processing assays, or diagnosing operational flaws in experimental platforms (e.g., PDMS compound absorption or Matrigel lot variability).
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Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Note: Guppy is deprecated; use Dorado for all new analyses.
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Computes a numeric or categorical answer to a quantitative data-science question by cleaning and analyzing local data files (CSV, Excel, TSV, and scientific formats .npz/.fits/.h5) with pandas, numpy, and scipy. Use whenever a task ships its own dataset (in whatever local directory it provides) and asks you to derive a value via statistical, geospatial, temporal, ratio, percentage, growth-rate, correlation, signal-processing, orbital, or forecasting analysis. Spans domains including archeology (demographics, paleoclimate proxies, radiocarbon dating, historical conflicts); biomedical/bioinformatics (tumor histology, genes, proteins, peptides, genomic variants); environmental (water quality, bacterial/Enterococcus exceedance, rainfall correlations, environmental justice); legal/consumer (fraud, identity theft, consumer complaints by state/metro); wildfire (incidents, causes, suppression costs, acres burned, fatalities, geospatial intersections); and astronomy/heliophysics/space weather (satellite telemetry TLE/Swarm/SP3, indices OMNI/GOES, solar activity, atmospheric density, orbital mechanics, forecasting).
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Functions, categories, and information. How mathematical objects relate to each other — morphisms, entropy, signal processing.
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Supreme policy layer governing all agent behavior. Autonomy, one-line prompt interpretation, speed standards, emphasis signal processing, cross-skill coordination, done definitions, conflict resolution. Loaded every prompt.
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Explains DSP math concepts to developers who need the theory behind an algorithm. Use whenever the user asks how a signal-processing concept works, wants intuition behind a formula, or hits a math-shaped bug. Trigger on phrases like "how does a Fourier transform work", "explain z-transforms", "what is convolution", "why does my biquad ring", "what is windowing for", "what causes aliasing", or "how do I convert gain to dB". Also trigger when the user pastes DSP code and asks why it behaves a certain way.
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Execute ENCODE ATAC-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Handles Tn5 transposase offset correction, mitochondrial read removal, and nucleosome-free fragment selection. Use when users need to process ATAC-seq data following ENCODE standards. Trigger on: ATAC-seq pipeline, run ATAC-seq, process ATAC-seq, chromatin accessibility, open chromatin, Tn5 shift, TSS enrichment.
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Fourier analysis specialist covering series, transforms, signal processing, and harmonic analysis
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An infographic skill for AI agents — works inside Claude Code, Codex, Hermes, OpenClaw, Cursor, and any agent host that loads skills. Create professional infographics as self-contained HTML files with PNG exports. Use when the user asks to create, design, generate, build, or make an infographic, data visualization, visual explainer, chart poster, cheatsheet, or pocket guide. Trigger phrases include "make this visual", "turn this into a graphic", "visualize this data", "infographic for X", "cheatsheet for X", or when the user provides structured data (tokenomics allocations, ecosystem/partner lists, timelines, comparisons, step-by-step processes) AND asks for a visual output. Covers tokenomics, ecosystem overviews, game overviews, cheatsheets, airdrop guides, comparisons, and process flows. Do NOT trigger for plain text answers, markdown tables, bulleted summaries, questions asking for advice or explanations about a topic (even when the topic is tokenomics, ecosystem, vesting, etc.), inline chat diagrams, or data processing with no visual output requested. The signal is "asks for a visual", not "mentions a keyword".
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