「junction」の検索結果

Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.

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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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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/MntJULiP/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q hyperparameter), OUTRIDER (gene-level outlier expression via autoencoder denoising), LeafcutterMD (Dirichlet-multinomial outlier mode of LeafCutter for annotation-free junctions), and DROP (Snakemake pipeline integrating FRASER2 + OUTRIDER + monoallelic expression for clinical diagnostics). The statistical model is fundamentally different from differential splicing — single-sample-vs-cohort outlier detection rather than two-group comparison. Standard tool in EU rare-disease (Solve-RD) and NIH UDN programs. Use when applying RNA-seq to undiagnosed Mendelian disease, validating predicted splice variants in clinical samples, or detecting cryptic splicing in disease tissue.

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Build RoadRunner HD Map entities in MATLAB — lanes, boundaries, markings, junctions, signs, signals, barriers, parking. Use when creating driving scenes from scratch, authoring road networks for simulation and testing automated driving systems, or assembling RRHD maps from Lanelet2 or other HD map sources.

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ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.

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The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across

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The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR package consists of a set of functions written in the R language in conjunction with C++. The efficiency of the package was confirmed by the examples of the analysis of RNA molecules fr

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Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.

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Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working wit

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Generate HeyGen presenter videos via the v3 Video Agent pipeline — handles Frame Check (aspect ratio correction), prompt engineering, avatar resolution, and voice selection. Required for any HeyGen video generation. Replaces deprecated endpoints with v3. Use when: (1) generating any HeyGen video (via API or otherwise), (2) sending a personalized video message (outreach, update, announcement, pitch, knowledge), (3) creating a HeyGen presenter-led explainer, tutorial, or product demo with a human face, (4) "make a video of me saying...", "send a video to my leads", "record an update for my team", "create a video pitch", "make a loom-style message", "I want to appear in this video", "generate a HeyGen video", "make a talking head video". Accepts avatar_id from heygen-avatar for identity-first HeyGen videos, or uses a stock presenter. Returns video share URL + HeyGen session URL for iteration. Chain signal: when the user wants to create/design an avatar AND make a video in the same request, run heygen-avatar first, then return here. Conjunctions to watch: "and then", "and immediately", "first...then", "X and make a video", "design [presenter] and record" = always CHAIN. If the user provides a photo AND wants a video, route to heygen-avatar first. NOT for: avatar creation or identity setup (use heygen-avatar first), cinematic footage or b-roll without a presenter, translating videos, TTS-only, or streaming avatars.

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Create original relaxed black-pen graphics from concepts or visual references, including sparse illustrations, narrative scenes, animals, objects, abstract relationships, icons, and logo marks. Use when the user wants quick hand-drawn line energy, causal story staging, non-equilibrium proportion, shorthand forms, open contours, structural line drift, misregistered junctions, selective retracing, physical pen texture, or a transferable illustration system that must not collapse into clean vector minimalism or polished period-sketch drawing.

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Analyze proof states in Isabelle or Coq and suggest applicable tactics to make progress. Use when users need help with: (1) Choosing the next tactic in an interactive proof, (2) Understanding what tactics apply to their current goal, (3) Getting unstuck in a proof, (4) Learning which tactics work for specific goal structures (conjunctions, implications, induction, etc.). Provides 3-5 ranked tactic suggestions with explanations for intermediate-level proofs in both Isabelle/Isar and Coq.

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Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.

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World-class database schema design - data modeling, migrations, relationships, and the battle scars from scaling databases that store billions of rowsUse when "database schema, data model, migration, prisma schema, drizzle schema, create table, add column, foreign key, primary key, uuid, auto increment, soft delete, normalization, denormalization, one to many, many to many, junction table, polymorphic, enum type, index strategy, database, schema, migration, data-model, prisma, drizzle, typeorm, postgresql, mysql, sqlite" mentioned.

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Probe the runtime state of a named feature flag in a CLI binary. Covers the four-pronged evidence protocol (binary strings, live invocation, on-disk state, platform cache), the four-state classification (LIVE / DARK / INDETERMINATE / UNKNOWN), gate-vs-event disambiguation, conjunction-gate handling, and skill-substitution scenarios where a flag appears DARK but the capability is delivered by other means. Use when verifying whether a documented or inferred capability has rolled out, when auditing dark-launched features, or when a prior probe's conclusions need refreshing against a new binary version.

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Classify gate call variants in a minified JavaScript bundle. Covers context-window extraction around a flag occurrence, identification of 4–6 reader variants (sync boolean, sync config-object, bootstrap-aware TTL, truthy-only, async bootstrap, async bridge), default-value extraction (boolean / null / numeric / config-object literal), conjunction detection across `&&` predicates, kill-switch inversion detection, and production of a gate-mechanics record that feeds probe- feature-flag-state. Use when a flag's behavior cannot be inferred from its name alone, when the binary uses multiple reader libraries, or when config-object gates carry structured schemas distinct from boolean gates.

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Use when configuring the Salesforce product catalog and pricing structure: creating Product2 records, setting up Standard and custom Pricebooks, managing PricebookEntry junction records, enabling multi-currency pricing, configuring Product Schedules (Revenue and Quantity), or troubleshooting incorrect prices on Opportunity line items and Quotes. Triggers: 'add product to pricebook', 'pricebook entry', 'standard pricebook', 'product catalog', 'multi-currency product pricing', 'product schedule', 'revenue schedule', 'quantity schedule', 'deactivate product'. NOT for bulk catalog loads — use data/product-catalog-data-model. NOT for CPQ bundles and product rules — use admin/cpq-product-catalog-setup.

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Designing Lookup vs Master-Detail vs Hierarchical vs External relationships: cascade delete, roll-up summaries, ownership, sharing implications, polymorphic lookups, junction objects, relationship depth limits. NOT for restricting which records a lookup can pick — use admin/lookup-filter-cross-object-patterns. NOT for a roll-up across a plain lookup — use data/roll-up-summary-alternatives.

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Use when creating a new Salesforce custom object: naming the object and setting its API name, selecting optional features (Activities, Chatter, History Tracking), choosing an org-wide default sharing model, and creating a tab. Triggers: 'create a custom object', 'new custom object setup', 'what sharing model should I choose', 'how do I create a tab for my object', 'object features like activities and history tracking'. NOT for designing the fields on the object - use admin/custom-field-creation. NOT for sharing rules or role hierarchy configuration - use admin/sharing-and-visibility. NOT for lookup-vs-master-detail and junction design - use data/data-model-design-patterns. More triggers: 'custom object records not showing in search', 'sharing model greyed out on my object', 'auto number restarted at 1 after deploy', 'cannot create a queue for my custom object', 'CustomObject deploy failed enableBulkApi', 'field history tracking shows no rows'.

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Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.

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Manage agent-skill lifecycles across local, global, project, Skill Hub, skills.sh, GitHub, plugin-cache, and system roots. Use when searching, recommending, installing, updating, upgrading, syncing, merging, auditing, deduplicating, cleaning, packaging, publishing, or validating skills; choosing project versus global scope; verifying upstream source, stars, or installs; or working with skill-upgrade, check_upstreams.ps1, sync-pull/push, junctions, skills-lock.json, or skill-upstreams.json. Do not use for ordinary software-package upgrades or non-skill file cleanup.

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End-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq. Aligns with STAR 2-pass cohort-style, performs junction QC (RSeQC, MaxEntScan, SpliceAI), runs rMATS-turbo and leafcutter for concordant differential analysis, optionally MAJIQ V3 for complex events / heterogeneous cohorts, isoform-switching with NMD/ORF/domain consequences (IsoformSwitchAnalyzeR v2 + DRIMSeq+DEXSeq+stageR DTU), and sashimi visualizations. Use when performing comprehensive splicing analysis from raw bulk RNA-seq data; for variant-driven splice prediction see splice-variant-prediction; for rare-disease single-patient outlier detection see outlier-splicing-detection; for full-isoform PacBio/ONT analysis see long-read-splicing.

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Controls the traffic-light actors on a running CARLA server — set a light green/red/yellow/off, freeze all lights (optionally all-green), set phase timing (green/yellow/red durations), and reset to the normal cycle. Target all lights, one by id, all in a junction, or the nearest. Use when the user asks to "make the light red", "freeze all lights green", "change the light timing", "turn the traffic lights off", or "reset the lights". This is the light actors, not the Traffic Manager (that's control-traffic).

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