「clo」の検索結果

Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - nearest-feature queries with signed/strand-aware distance, fixed-radius window searches, strand-aware promoter construction, and interval extension. Covers the closest -d/-D a/b/ref/-t/-k/-io/-iu/-id flags, the -D ref strand sign-flip, silent chromosome-end clipping in slop/flank, -t all tie double-counting, and the critical distinction between a geometry answer (nearest TSS) and a biology answer (which gene an element regulates). Use when assigning peaks or variants to genes, defining promoters from a gene model, building distance-to-TSS distributions, finding features within a window, or extending intervals - and when deciding whether nearest-gene is a fair prior (GWAS locus) or a trap (distal enhancer).

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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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Designs pooled sgRNA libraries for CRISPR knockout, interference (CRISPRi), activation (CRISPRa), Cas12a multiplex, base-editor, and prime-editor screens. Covers on-target scoring (Rule Set 2, Azimuth, DeepSpCas9, CRISPRon), off-target scoring (CFD, MIT), TSS-relative positioning for CRISPRi/a (Horlbeck, Dolcetto, Calabrese), PAM-variant chemistries, control-guide composition, oligo cloning architecture, and library QC. Use when choosing a genome-wide library (GeCKOv2 vs Avana vs Brunello vs TKOv3 vs Inzolia), designing a focused or paralog-focused custom library, picking CRISPRi vs CRISPRa TSS windows, deciding control-guide proportions, or diagnosing library skew and dropout in a freshly cloned pool.

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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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Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror. Use when pulling FASTQ for SRR/ERR/DRR accessions, deciding between SRA-direct, ENA mirror, or AWS/GCP cloud mirror (STRIDES), handling --include-technical for 10x and other single-cell records, validating with MD5/vdb-validate, navigating SRR/SRX/SRS/SRP/PRJNA hierarchy, or finding accessions via pysradb. Encodes SRA cloud-egress economics, the fasterq-dump uncompressed-scratch trap, and the --max-size default that silently truncates large prefetches.

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Use when working with ANY data persistence, database, storage, CloudKit, migration, or serialization in an Apple app. Covers SwiftData, Core Data, GRDB, SQLite, Realm, CloudKit sync, file storage, Codable, migrations.

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Build or maintain Cloudflare Sandbox apps on @cloudflare/sandbox@next (SDK 1.0 preview). Use sandbox-migrate-to-next when porting a stable app.

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Deploys and operates a LiveKit agent in production: shipping a version to LiveKit Cloud and rolling it back, secrets and configuration, the worker process model and prewarming, safe async inside worker processes, provider timeouts and degradation, graceful shutdown, SDK upgrades, and observability. Use when the user says "deploy my agent", "roll back the deployment", "tail the agent logs", "the first call after a restart is slow", "attached to a different loop / event loop is closed", "prewarm the VAD", "shut down without dropping calls", "upgrade livekit-agents safely", "correlate logs by session", or is changing an agent codebase that is already live. Not for designing the agent (building-livekit-agents) or reproducing one bad conversation locally (debugging-livekit-agents).

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Assess and plan migrations from existing VPN, SWG, or SASE platforms to Cloudflare One, including policy mapping, parity gaps, and rollout.

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Build or maintain Cloudflare Sandbox apps on the stable @cloudflare/sandbox package. Use sandbox-next for preview apps and sandbox-migrate-to-next for stable-to-preview migrations.

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Implement or troubleshoot Cloudflare Email Sending and Email Routing integrations and their delivery configuration.

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Translate NI-DAQmx C function signatures into correct calldaqlib MATLAB calls. Use when the user mentions calldaqlib, any DAQmx* C function name (DAQmxCfgSampClkTiming, DAQmxExportSignal, DAQmxSetStartTrigRetriggerable, DAQmxGetSampClkRate, etc.), or needs NI-DAQmx functionality not exposed by the daq object. Covers: projection rules (taskHandle implicit, output pointers become return values, buffer-size args, enum-as-string), multi-task semantics, start() clobber, device-level empty-daq workaround, dictionary returns, string getter placeholder, array getter placeholder. Trigger contexts: low-level DAQ, escape hatch, retriggerable acquisition, shared timebase, export signal, connect terminals, external sample clock, trigger configuration, NI driver, C function translation.

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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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Analyze AMS waveform data using Mixed-Signal Blockset utilities: phase noise measurement, clock jitter, anti-aliased resampling, timing measurements, lock time, INL/DNL, ADC/DAC calibration, HSpice import. Use when analyzing time-domain voltage from PLL/VCO/clock simulations, measuring phase noise from variable-step solver output, computing jitter, or resampling non-uniform data.

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Foundation skill for all RoadRunner workflows: MATLAB path setup, connection, project/scene/scenario lifecycle, world settings, handle management, status, and close. Use when connecting to RoadRunner, managing projects/scenes/scenarios, setting world origin, checking status, closing RoadRunner, or when any downstream RoadRunner skill needs initialization.

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AWS CloudFormation infrastructure as code for stack management. Use when writing templates, deploying stacks, managing drift, troubleshooting deployments, or organizing infrastructure with nested stacks.

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AWS CloudWatch monitoring for logs, metrics, alarms, and dashboards. Use when setting up monitoring, creating alarms, querying logs with Insights, configuring metric filters, building dashboards, or troubleshooting application issues.

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AWS EC2 virtual machine management — instances, security groups, key pairs, AMIs, EBS volumes, Auto Scaling Groups, Spot Instances, Session Manager, placement groups, and instance lifecycle automation. Trigger on ANY of these, even when EC2 isn't named explicitly: - Launching or provisioning: "spin up a server", "create a VM", "new instance", "run-instances", mention of instance types (t3, m5, c5, r6, g5, p4d, t4g, c7g, etc.) - SSH / connectivity problems: "connection refused", "connection timed out", "permission denied publickey", "can't connect to my instance", "SSH not working" - Instance management: resize, stop, start, terminate, reboot, change instance type - Cost optimization: stop dev instances overnight, save money on EC2, spot vs on-demand, reserved instances - Auto Scaling: ASG, launch template, mixed instances policy, scale to zero, scheduled scaling - Spot Instances: spot fleet, spot interruption, capacity-optimized, price-capacity-optimized - AMIs and backups: create image, custom AMI, EBS snapshot, DLM lifecycle policy, copy AMI - Monitoring: EC2 CPU utilization, CloudWatch metrics for instance, instance status checks, console output - Access methods: Session Manager, EC2 Instance Connect, bastion host, port forwarding - Security: IMDSv2, instance metadata, IAM role on instance, security group rules - User data and bootstrap scripts, cloud-init

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Configure CDNs for content delivery. Set up CloudFront, Cloudflare, and Fastly. Use when optimizing global content delivery.

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Build and deploy edge functions with Cloudflare Workers and Wrangler. Use for APIs, cron jobs, and edge middleware.

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。

Provision Cloud SQL and Spanner databases. Configure high availability, backups, and security. Use when deploying managed databases on GCP.

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。

Deploy serverless functions on Google Cloud Functions. Configure triggers and manage deployments. Use when implementing serverless workloads on GCP.

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Protect internal apps with Cloudflare Access, device posture, and Zero Trust policies.

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Manage Cloudflare R2 buckets, lifecycle, and signed URLs. Use for low-egress object storage and media delivery.

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。