「fact」の検索結果

Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy framework, factor decomposition, genome-scale Perturb-seq (Replogle 2022 Cell, 2.5M cells), and per-perturbation single-cell DE. Use when running a single-cell CRISPR screen, choosing direct-capture vs CROP-seq architecture, filtering escaper cells, performing single-cell DE, integrating Perturb-seq with pathway analysis, scaling to GW CRISPRi via Replogle protocol, or analyzing multi-omics screens.

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。

Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.

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。

Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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。

Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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。

Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Handles peak stitching parameters, ranking choices, hockey-stick inflection, marker choice (H3K27ac vs MED1/BRD4), and cross-condition comparison with spike-in normalization. Constructs core regulatory circuitry (Saint-Andre 2016) from SE-encoded TFs. Use when identifying cell-identity / cancer-associated regulatory domains, comparing super-enhancers between conditions, identifying master transcription factor networks, or predicting BET-inhibitor responsiveness.

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。

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, and applies the Patel et al 2024 *Nat Biotechnol* review's failure-mode framework to validate that normalization is correctly 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.

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。

Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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。

Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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。

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 2025 Nat Genet; 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.

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。

Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

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。

ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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。

Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3/SQANTI-LR (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

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。

Use this skill to design a vehicle preventive maintenance schedule. Covers manufacturer recommendations, industry-standard intervals, and how to set carrier-specific triggers.

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。

Use this skill when the user asks about truck purchase financing, leasing options, factoring, fuel surcharge math, lease-purchase agreements, the total-cost-of-ownership (TCO) comparison between buying + leasing, and how owner-operators finance their first truck. Cover Section 179 + Bonus Depreciation tax treatment.

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。

Use this skill to calculate Working Load Limits for cargo tiedowns. Covers manufacturer ratings, deration, and total tiedown WLL.

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。

Use this skill when the user asks about accident claims management — first-notice-of-loss procedures, working with insurance adjusters, claim severity classification, subrogation, claim closure timelines, and how to influence claim outcomes. Different from accident-investigation-playbook (which covers facts); this covers the insurance + claim side.

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。

Use this skill when the user asks the difference between a freight broker, freight forwarder, and motor carrier (49 CFR 371 + 373) — required authority for each, bond requirements (BMC-84 broker bond, BMC-85 freight forwarder bond), broker-carrier agreements, factoring + commissions, double brokering, and how to identify each role on a Bill of Lading. Cite 49 CFR 371 + 373.

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。

Propose a new change with all artifacts generated in one step. Use when the user wants to quickly describe what they want to build and get a complete proposal with design, specs, and tasks ready for implementation.

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。

Sizing tokens for compact sidebars, nav panels, and menu lists. Use when building or refactoring a sidebar, settings menu, category list, filter bar, or expandable nav tree, or when a sidebar looks too wide, too padded, or wastes space.

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。

Agent fallback for CEngineServer_ClientPrintf-decompiles (auto-generated, category: vfunc). Locate CEngineServer::ClientPrintf in the CS2 engine module via IDA Pro MCP and emit a fresh, minimal-unique artifact. The deterministic preprocessor could not resolve this symbol on the current gamever - your job is the re-sign. Trigger: CEngineServer_ClientPrintf-decompiles, CEngineServer::ClientPrintf

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。

Agent fallback for CEngineServer_GetClientConVarValue (auto-generated, category: vfunc). Locate CEngineServer::GetClientConVarValue in the CS2 engine module via IDA Pro MCP and emit a fresh, minimal-unique artifact. The deterministic preprocessor could not resolve this symbol on the current gamever - your job is the re-sign. Trigger: CEngineServer_GetClientConVarValue, CEngineServer::GetClientConVarValue

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。

Agent fallback for CEngineGameUI_vtable (auto-generated, category: func). Locate CEngineGameUI_vtable in the CS2 engine module via IDA Pro MCP and emit a fresh, minimal-unique artifact. The deterministic preprocessor could not resolve this symbol on the current gamever - your job is the re-sign. Trigger: CEngineGameUI_vtable, CEngineGameUI_vtable

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。

Agent fallback for CEngineClient_DumpNetStats (auto-generated, category: vfunc). Locate CEngineClient::DumpNetStats in the CS2 engine module via IDA Pro MCP and emit a fresh, minimal-unique artifact. The deterministic preprocessor could not resolve this symbol on the current gamever - your job is the re-sign. Trigger: CEngineClient_DumpNetStats, CEngineClient::DumpNetStats

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。

Agent fallback for CEngineServer_IsMapValid-inlined (auto-generated, category: vfunc). Locate CEngineServer::IsMapValid in the CS2 engine module via IDA Pro MCP and emit a fresh, minimal-unique artifact. The deterministic preprocessor could not resolve this symbol on the current gamever - your job is the re-sign. Trigger: CEngineServer_IsMapValid-inlined, CEngineServer::IsMapValid

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。