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概要と使いどころ
Daily industry intelligence scanner. Scans web, social media, news, blogs, and communities for industry-relevant events, trends, and signals. Produces a comprehensive intelligence briefing plus strategic GTM opportunity ideas. Orchestrates existing scraping skills — does not reimplement data collection.
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Designs and ranks guide RNAs (sgRNAs) for CRISPR-Cas9/Cas12a gene knockout by scanning a target for PAM sites (NGG SpCas9, NNGRRT SaCas9, TTTV Cas12a, NG SpCas9-NG, near-PAMless SpRY), enumerating candidate spacers, applying hard filters (Pol-III TTTT terminator, 5' G, GC), ranking on-target activity with the context-appropriate model (Rule Set 2/Azimuth for U6/lentiviral, CRISPRscan for T7/embryo, DeepHF for high-fidelity variants, DeepCpf1 for Cas12a), and predicting the indel/frameshift outcome (Bae out-of-frame score, inDelphi, FORECasT, Lindel). Use when selecting sgRNAs to knock out a gene, choosing a nuclease/PAM for a constrained locus, picking which exon to target, or shortlisting guides before an off-target check. Off-target specificity, base/prime editing, and HDR donors are separate skills.
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Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate candidate CD8 T-cell epitopes. Covers the binding-affinity (BA) vs eluted-ligand (EL/presentation) distinction, why %Rank beats raw nM for cross-allele work, the MS abundance bias that misranks low-expression neoantigens, allele-coverage inequity, and length bias. Use when scanning a protein or peptide set for class I epitopes, scoring neoantigen candidates, or choosing a binding predictor. For CD4/HLA class II see mhc-class-ii-prediction.
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Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools computeMatrix scale-regions), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (log2 IP/input bigWig via deepTools bamCompare; pyGenomeTracks; Gviz; IGV/UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), feature-distribution stacked bars, and volcano/MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012; Meyer 2012). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features, generating DRACH motif logos as sanity checks, rendering volcano plots of differential m6A, or reproducing the stop-codon enrichment plot.
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Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement, and axis-truncation conventions. Covers EnhancedVolcano, ggplot2, matplotlib, and the apeglm/ashr/normal shrinkage decision. Use when visualizing differential-expression results (RNA-seq, ChIP-seq, ATAC-seq, proteomics) or any per-feature effect-size + p-value table.
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Standardizes molecular structures using the ChEMBL structure pipeline for normalization and parent selection plus RDKit rdMolStandardize for explicit custom steps such as tautomer canonicalization, salt/solvent stripping, charge handling, stereochemistry handling, mixture selection, and isotope normalization. Explicitly compares ChEMBL, canSARchem, RDKit, and PubChem standardization choices. Use when preparing libraries for QSAR training, joining datasets across sources, deduplicating compound collections, or building canonical compound registries.
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Runs cis-pQTL Mendelian randomization for drug-target validation using UKB-PPP (Olink), deCODE (SomaScan), Fenland, INTERVAL, ARIC, and FinnGen-PPP proteomes plus colocalization triangulation, phenome-wide on-target adverse-effect scans, cross-platform Olink/SomaScan replication, and PAV (protein-altering variant) sensitivity. Use when nominating or de-risking a drug target from plasma-proteome GWAS, mimicking pharmacological inhibition via cis-pQTL instruments, separating shared-causal from LD-confounded signal under the Schmidt 2020 cis-MR framework, screening on-target adverse phenotypes pheWAS-style, or producing publication-grade STROBE-MR plus PP.H4 evidence for a target gene.
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Discover, configure, and connect to Arduino boards from MATLAB using the Arduino Support Package. Use this skill when the user wants to set up an Arduino board, connect to Arduino hardware, find connected boards, scan serial ports, configure Arduino libraries, or any task that requires an Arduino connection as a prerequisite (e.g., blink LED, read sensor, read digital pin, read analog pin, write pin, plot sensor data, scan I2C, use ultrasonic sensor, control servo, read temperature, read voltage, data logging from hardware). Triggers on: arduino, board setup, COM port, serial port, hardware connection, Arduino Nano, Arduino Uno, Arduino Mega, Arduino Micro, Grove, sensor setup, I2C scan, ultrasonic, servo, readDigitalPin, writeDigitalPin, readVoltage, writePWMVoltage, temperature sensor, air pressure, pin read, pin write, analog input.
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Use when setting up vehicle network communication in MATLAB using Vehicle Network Toolbox. Covers CAN/CAN FD (fully implemented), with architecture for J1939, XCP, and future protocols. Handles hardware discovery, channel creation, bus configuration, message exchange, signal encoding/decoding, and analysis across all supported vendors. (Vector, Kvaser, PEAK-System, NI, SocketCAN, MathWorks Virtual).
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Port MATLAB Data Acquisition Toolbox code from the discouraged (legacy) session-based interface (daq.createSession, addAnalogInputChannel, startBackground, DataAvailable listeners, queueOutputData, wait) to the recommended DataAcquisition interface (daq("ni"), addinput, start, ScansAvailableFcn, write, preload). Use when migrating legacy DAQ scripts, converting session-API calls, working with DataAcquisition objects, writing multi-feature DAQ scripts that combine triggers, callbacks, continuous acquisition, or analog output. Also use when a user says their DAQ script "used to work" or "errors on R20XX", since modernizing legacy session-API code is a frequent fix for those failures. Trigger keywords: daq, DAQ, NI, session interface, addtrigger, addclock, ScansAvailableFcn, ScansRequiredFcn, daq.createSession, addAnalogInputChannel, startBackground, queueOutputData, DataAvailable, evt.Data, evt.TimeStamps, wait(d), preload, discouraged, legacy, modernize, R2020a.
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Detect and validate GPU availability for MATLAB GPU computing. Use when the user can't use their GPU, or is setting up or selecting a GPU. Triggers on: gpuDevice, GPU setup, check GPU, GPU not found, GPU not working, can't use GPU, GPU not available, unable to find a supported GPU device, compatible GPU, canUseGPU, validateGPU.
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Discover MATLAB Parallel Computing Toolbox clusters on the network and in the cloud, and manage their profiles — list, inspect, import, export, set default, validate, and delete. Use whenever the user asks what parallel computing resources, clusters, or cluster profiles they have or can use — e.g. "what parallel resources do I have", "show my cluster profiles", "list clusters", "what clusters can I run on", "where can I submit jobs" — and for any work with parcluster, parallel.listProfiles, parallel.defaultProfile, MJS / Generic / HPC Server / MJSComputeCloud clusters, .mlsettings files, or profile validation. Does NOT cover job submission, parpool, or parfor.
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Scan systems and dependencies for CVEs and security vulnerabilities. Use tools like Nessus, OpenVAS, and Qualys to identify and prioritize vulnerabilities. Use when performing security assessments, compliance scanning, or vulnerability management.
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Scan agent skills for security issues. Use when asked to "scan a skill", "audit a skill", "review skill security", "check skill for injection", "validate SKILL.md", or assess whether an agent skill is safe to install. Checks for prompt injection, malicious scripts, excessive permissions, secret exposure, and supply chain risks.
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Audit existing content across a site to decide what to keep, update, merge, redirect, or delete. Use this skill whenever the user wants to audit existing content, fix content decay, resolve keyword cannibalization, prune underperforming pages, prioritize content updates, or apply a keep/update/merge/redirect/delete framework to a content library. Triggers on content audit, content decay, content refresh, cannibalization, keyword cannibalization, prune content, delete pages, redirect old pages, content inventory, what to keep, what to update, content scorecard, evergreen refresh. Also triggers when traffic is dropping site-wide and the cause might be content quality, even if 'audit' is not said explicitly.
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Produces an adversarial attack on a legal argument that survives reply. Runs the opposing-counsel discipline twice: an unrestrained first pass, then the same instrument turned on that pass to cut every point that collapses under challenge - attacks on conceded facts, wrong-forum objections, speculation about documents and motives, gotchas with innocent explanations, overclaims, self-refuting assertions, and padding. The deliverable is one standalone attack containing only what can be defended, capped at five heads, not a discussion of the discarded draft. Use to attack, stress-test, red-team or rebut a submission, brief, motion, witness statement, letter or structured legal reasoning. Triggers on "attack this but only with points that hold", "no cheap shots", "what survives reply", "which points can I actually defend", "give me the version I can file", "double-pass adversarial review". Also use when an earlier adversarial review came back overlong or scattershot. Formal British English.
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Run an attorney-facing knockout/availability trademark search across the United States and Canada. Use whenever a user (founder, client, or attorney) asks whether a brand, mark, name, logo, slogan, or product name is "available," "free to use," "clearable," or "already taken" — or asks Claude to "search the trademark register," "check USPTO," "check CIPO," "do a knockout search," "clearance search," "availability search," or "see if [mark] is trademarked." Trigger even when the user phrases it casually ("can I call my company X?", "is this name taken?"). Covers federal USPTO (TESS/TSDR), federal Canada (CIPO), common-law/web/state, and WIPO Madrid international. Output is a knockout availability memo with green/yellow/red verdict for attorney review. Includes professional-responsibility gating (AI-use disclosure, conflict check, scope confirmation) before substantive analysis. Not legal advice — produces work product for attorney sign-off.
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Professional network reconnaissance and port scanning using nmap. Supports various scan types (quick, full, UDP, stealth), service detection, vulnerability scanning, and NSE scripts. Use when you need to enumerate network services, detect versions, or perform network reconnaissance.
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A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).
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A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.
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This package enables the interpretation and analysis of results from a gene set enrichment analysis using network-based and text-mining approaches. Most enrichment analyses result in large lists of significant gene sets that are difficult to interpret. Tools in this package help build a similarity-based network of significant gene sets from a gene set enrichment analysis that can then be investigated for their biological function using text-mining approaches.
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SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. You can either use your own single-cell study for the simulation or the sfaira database. Different pre-defined simulation scenarios exist, as are options to run custom simulations. Additionally, expression values can be adapted by adding an mRNA bias, which produces more biologically relevant simulations.
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This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. In contrast to TDbasedUFE which can perform simple the feature selection and the multiomics analyses, this package can perform more complicated and advanced features, but they are not so popularly required. Only users who require more specific features can make use of its functionality.
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syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-bas
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