「library」の検索結果

Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for visualisation.

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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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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Nat Commun 12:1302), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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Analyzes base-editing screens for variant function. Covers library design (Hanna 2021 ClinVar-scale CBE screen benchmarked on BRCA1/2, Cuella-Martin 2021 DDR saturation), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end; 4-7 for ABE7.10), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.

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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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Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

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Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.

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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, applies the Patel et al 2024 *Nat Biotechnol* failure-mode framework, and validates that normalization is applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, MHFP6 LSH forest, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

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Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.

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Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory features and ELBO_gain test), scQuint (junction-cluster, plate-based; not for 10X), SpliZ (annotation-free Z-score), Psix (graph-smoothness regulated AS), and Sierra (alternative polyadenylation, often confused with AS). Use when analyzing isoform usage in scRNA-seq, identifying cell-type-specific splicing, or determining whether scRNA-seq chemistry supports splicing analysis at all.

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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.

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Use when working with camera, photos, audio, haptics, ShazamKit, on-device music analysis, face grouping and video highlights, screen recording, casting to non-AirPlay routes, SharePlay playback, the user's Apple Music library, lock-screen metadata, or CarPlay app design, templates, and navigation. Covers AVCaptureSession, AVFoundation, Core Haptics, MediaPlayer, MusicKit, NowPlaying, ScreenCaptureKit, DockKit.

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Integrate Apple Pay payments and Wallet passes using PassKit. Use when adding Apple Pay buttons, creating payment requests, handling payment authorization, adding passes to Wallet, configuring merchant capabilities, managing shipping/contact fields, or working with PKPaymentRequest, PKPaymentAuthorizationController, PKPaymentButton, AddPassToWalletButton, PKPass, PKAddPassesViewController, PKPassLibrary, Wallet pass distribution, or Apple Pay checkout flows for physical goods, real-world services, donations, and eligible recurring payments.

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Set up worker environment and per-worker state for parallel pools. Use when code needs paths, environment variables, database connections, loaded libraries, or expensive objects available on workers before parfor/parfeval runs. Teaches parallel.pool.Constant, parfevalOnAll, and parpool name-value pairs. Also use when refactoring existing code that uses spmd for side-effect setup (an anti-pattern). Triggers: worker setup, pool constant, per-worker state, non-serializable, loadlibrary on workers, database connection parfor, addpath workers, spmd before parfor, worker environment, reduce parfor overhead, parfor setup, resource creation in parallel loop, cannot serialize error, undefined function or variable on workers error, load data per worker, reduce data transfer, parallelize setup, improve parallel code.

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Build, import, analyze, tolerate, and optimize optical systems using the Optical Design and Simulation Library. Use when the user asks about optical systems, ray tracing, geometric optics, Zemax import, optical coatings, tolerancing, or optical design optimization.

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Build Simulink models that co-simulate with Eclipse SUMO traffic simulator. Use when creating SUMO-Simulink co-simulation, traffic simulation, TraCI connection, vehicle-in-the-loop testing, or ADAS scenario validation with SUMO. Covers Server/Client setup, Reader/Writer/Actor block configuration, random traffic generation, ego vehicle control, and SUMO file creation. Also use when the user mentions SumoInterfaceLibrary, .sumocfg files, or wants to connect Simulink to an external traffic simulator.

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Use when evaluating whether a skill belongs in a library. Preview content, check frontmatter, validate structure, and decide whether to keep, curate, or remove.

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Use when regenerating README.md and WORK_AREAS.md in a managed library workspace. Always dry-run first to preview changes.

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Verify claims, quotations, citations and references against live primary sources, and produce a reproducible audit record instead of an assertion. Use when asked to: check whether a quotation, verse, statistic, date, attribution or citation is accurate; verify references before publishing a report, thesis, article, slide deck or legal filing; confirm a text against an authoritative database; cross-check a claim across independent sources; build a citation register or verification appendix; find out whether two datasets agree; detect a misattributed or fabricated quotation; or audit a document's existing citations. Source-agnostic by design, with working providers for REST/JSON APIs, scraped HTML, bulk corpora, bibliographic catalogues (OpenLibrary), DOI resolution (Crossref) and reference works (Wikipedia) -- including scriptural tiers (Qur'an.com, sunnah.com and an independent hadith corpus) with full diacritic handling for Arabic, Hebrew, Greek and any script with optional marks. Covers content-addressed matching when sources disagree on numbering, graded match verdicts, byte-level integrity checks, published-string verification, and a catalogue of silent failure modes (identifier divergence, mojibake, scraper blocking, false-positive keyword rules, missing glyphs, unreliable PDF text layers).

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Use when a SPEC, INNOVATE, or VALIDATE (Layer 2) approach hinges on an unverified runtime/library/external mechanism: run a probe from the 8-family taxonomy and produce a VIABLE/NOT-VIABLE/INCONCLUSIVE VERDICT artifact.

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Sync, validate, and apply App Store metadata and store assets with asc. Use when updating localizations, keywords, App Clip or preview assets, Asset Library media and placements, or migrating legacy fastlane metadata.

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Use when generating sexy/NSFW or posed images with local Qwen-Image 2.1 — pose/NSFW LoRAs (tawsLoRa femaledVaginus, TheseAlpacas, posture-v3), pose transfer from an existing image, or exact pose control via VNCCS PoseStudio 3D pose library. Triggers: 性感姿势, 摆姿势, NSFW 出图, 换姿势, 姿势控制, pose transfer, pose lora, VNCCS, 人偶姿势, 姿势库. Independent of any general image-generation skill (which handles SFW text/edit/cutout work).

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