「cover」の検索結果

Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM), MeTPeak (HMM over sliding windows), MACS3/MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody methods cannot resolve, and orthogonal validation (miCLIP/GLORI/m6A-SAC-seq/m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set, reconciling differing peak sets across tools, validating MeRIP peaks against single-base methods, interpreting 5' peaks where m6Am contamination is possible, or recommending a consensus strategy.

日本語の概要は準備中です。原文の説明を表示しています。

Discovers, classifies, and masks repetitive elements and transposable elements with RepeatModeler2 (de novo family library), RepeatMasker (masking against a library), EDTA (plant/structural TEs), or EarlGrey (auto-curating wrapper), and quantifies TE expression from RNA-seq with TEtranscripts/SQuIRE. Covers de-novo-library-as-curation-project, soft-vs-hard masking, the domesticated-gene over-masking massacre, Dfam-vs-RepBase, TE classification (Class I/II, family-vs-copy), Kimura repeat landscapes, LAI, and the RNA-seq multimapping problem. Use when masking repeats before gene prediction, building a TE library for a non-model genome, or analyzing transposable-element content or expression.

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Designs and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Covers bottleneck math (250x cells/sgRNA requires ~25M cells implanted; impossible for most syngeneic models, forcing focused libraries), focused library design (Manguso 2017 Nature 547:413 immune screen; Chen 2015 tumor screens), CRISPR-StAR intrinsic-control screening (Uijttewaal 2025 Nat Biotechnol 43:1848), clonal-dynamics-limited detection, tumor-explant DNA recovery, syngeneic vs xenograft vs PDX considerations, and the relationship to downstream MAGeCK / drugZ analysis. Use when designing in vivo CRISPR screens for tumor / immune / metastasis biology, choosing focused vs genome-wide for animal models, addressing bottleneck-induced clonal collapse, picking the syngeneic / xenograft / PDX model, integrating in vivo with in vitro results, or applying CRISPR-StAR for animal experiments.

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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.

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Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.

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Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2024 bioRxiv; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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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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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

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Discover and configure Bluetooth and Wi-Fi accessories using AccessorySetupKit. Use when presenting a privacy-preserving accessory picker, defining discovery descriptors for BLE or Wi-Fi devices, handling accessory session events, migrating from CoreBluetooth permission-based scanning, or setting up accessories without requiring broad Bluetooth permissions.

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Writes turn-level tests for a LiveKit agent in the user's normal test suite: pytest (Python) or Vitest (Node.js). Use when the user asks to "write tests for my agent", "add a test for this tool", "test the handoff", "pin this bug", "why does my agent test fail", or after building or changing agent behavior that needs regression coverage. Covers the SDK's test session harness, assertions on messages, tool calls and handoffs, LLM judging of a reply against an intent, mocking tools, multi-turn tests, and judging whole conversations with the built-in judges. For interactive poking use debugging-livekit-agents. For grading whole conversations at scale use running-livekit-simulations.

日本語の概要は準備中です。原文の説明を表示しています。

Builds voice and chat AI agents with LiveKit Agents on LiveKit Cloud or a self-hosted server. Use when the user asks to "build a voice agent", "create a LiveKit agent", "add voice AI to my app", "implement handoffs", "structure an agent workflow", "my agent is slow / too chatty", "it says it booked but nothing was saved", "make it confirm before committing", "it keeps re-asking things the caller already said", or is writing code against the LiveKit Agents SDK. Covers architecture: designing for latency, keeping context small, splitting a monolithic agent into handoffs and tasks, and designing for voice. Also covers keeping the model in charge of meaning while code owns state, approvals, and effects. For API specifics use reading-livekit-docs. To check behavior use debugging-livekit-agents and testing-livekit-agents.

日本語の概要は準備中です。原文の説明を表示しています。

Set up and verify a connection to an NI USRP radio (USRP E320, N300, N310, N320, N321, X300, X310, or X410) using Wireless Testbench. Use when connecting a USRP for the first time, configuring radio hardware, troubleshooting connection failures, or verifying a radio setup. Covers host inspection (OS, NIC type/speed/MTU), device discovery (findsdru, probesdru), UHD version checking, programmatic radio configuration, and basebandTransceiver verification. Also use when the user mentions USRP setup, radio not found, connection errors, dropped samples, or network configuration for SDR hardware.

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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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Establish MAVLink connections between MATLAB and PX4/ArduPilot autopilots. Use when connecting to a drone, flight controller, or autopilot via MAVLink protocol over UDP. Covers dialect setup, UDP transport, timer-based heartbeat, and client discovery. Use when: "connect to PX4", "MAVLink connection", "heartbeat", "ground control station", "GCS", "connect to ArduPilot", "drone communication", "mavlinkio", "SITL".

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Discovers connected MATLAB-supported hardware devices, searches by capability, and checks required support packages and add-ons. Use when the user asks what hardware is connected, finds a device that supports a capability (e.g., CAN, analog input), or checks if required support packages or add-ons are installed. Does NOT connect to, configure, or acquire data from devices — defers to device-specific skills for usage workflows.

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Guide users or agents to the correct MATLAB tool for processing large tabular data in file-based formats (CSV, Parquet, delimited text, spreadsheets, MDF) that may not fit in memory. Use when a user or agent mentions large files, big data, out-of-memory errors, OOM, scaling up, tall arrays, datastores, or needs to process multiple tabular files. Covers the decision between datastore + tall, datastore + transform, and parallel execution. Also use when a user or agent has working in-memory code (readtable, parquetread) that runs out of memory and needs a migration path. Also covers building custom datastore classes for proprietary or non-standard formats — use when the task requires subclassing matlab.io.Datastore, implementing a custom reader, building an extensible datastore, or integrating a new file format with tall arrays or parallel computing. Do NOT use for MAT files (use matfile instead).

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Store, retrieve, and pass credentials securely in MATLAB using the built-in MATLAB Vault (setSecret, getSecret, importSecrets, secretID) instead of hardcoding. Handles connections to any authenticated service: REST APIs, databases, cloud storage (S3/Azure/GCS), SFTP, and others. Covers API keys, tokens, passwords, SSH passphrases, CI/batch/scheduled jobs, and "keep credentials out of code" requests. Does NOT cover third-party secret managers (HashiCorp Vault, AWS Secrets Manager), OS-level key management, or the connection/query logic itself.

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Implement backup and recovery strategies. Configure rsync, Restic, and cloud backups. Use when designing data protection solutions.

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Implement database backup strategies. Configure automated backups, retention, and recovery testing. Use when designing backup and recovery procedures.

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Implement disaster recovery strategies and runbooks. Configure RPO/RTO targets and failover procedures. Use when planning for business continuity.

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Discover and load all relevant context for the current task. Lists feature group nested files with full paths, loads process/context/ files by domain routing. Called at the start of every agent session.

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Discover profitable business ideas from scratch. Analyzes market gaps, trending niches, user skills, and competitive landscapes with a competitive intelligence protocol including 4-filter benchmark stress test and Blue Ocean differentiation grid. Use when the user has no idea what to build, wants to explore opportunities, needs market research, competitive benchmarking, or says 'find me a business idea', 'what should I build', 'market research', 'find opportunities', or 'competitive analysis'.

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Codify a successful workflow from the current conversation into a permanent project-local skill. After you discover (e.g.) a cold-email sequence that converts, an ad-creative format that beats baseline, or a content-pipeline cadence that compounds — /money-skillify writes it as a SKILL.md under the project's local skills directory so future sessions can re-invoke it without re-discovery. Use when the user says: 'this worked, save it', 'codify this', 'turn this into a skill', '把这个固化下来', '存成 skill'.

日本語の概要は準備中です。原文の説明を表示しています。