「nature」の検索結果

Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot with 5'UTR / CDS / 3'UTR scaling; MetaPlotR; deepTools `computeMatrix scale-regions`), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (bigWig of log2 IP/input via deepTools `bamCompare`; ggcoverage; pyGenomeTracks; Gviz; IGV / UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), 5'UTR / CDS / 3'UTR stacked-bar feature-distribution summaries, and volcano / MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012 *Nature* 485:201; Meyer 2012 *Cell* 149:1635 — concurrent founding papers from different labs both showed this independently). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features for figure 1, generating DRACH motif logos as sanity checks on the peak set, rendering volcano plots of differential m6A, or reproducing the Dominissini 2012 / Meyer 2012 stop-codon enrichment plot.

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Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart 2017), Cas9 cut-toxicity diagnostics, copy-number amplicon detection (Aguirre 2016 / Munoz 2016), bottleneck propagation through plasmid pool, infection, selection, and endpoint stages, MOI verification, and DepMap-style screen-quality scoring. Use when assessing screen quality before hit calling, deciding whether to repeat or rescue a screen, diagnosing low-confidence hits, choosing between MAGeCK / BAGEL2 / Chronos based on quality grade, picking a normalization strategy from QC signatures, or evaluating whether an in-vivo screen retained adequate library complexity.

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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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Compose multi-panel publication figures with patchwork, cowplot, gridExtra (R), or matplotlib GridSpec/subfigures (Python) including shared axes/legends/guides collection, panel labels in Nature/Cell convention, and journal-spec sizing. Covers patchwork ≥1.2.0 axes='collect' feature, Type-42 font embedding, and the cairo_pdf save path. Use when composing 2+ subpanels into a single figure for journal submission.

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Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.

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Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware), MSIngs, MANTIS, MSIPanel, MSIDetect, and ngsMSI for FDA pembrolizumab MSI-H pan-tumor / Lynch syndrome / dMMR ICI biomarker. Use when stratifying ICI eligibility (Le 2015), pairing MSI with TMB-H (Sha 2020 / Salem 2018), screening Lynch syndrome (universal IHC + MSI), or distinguishing MSI-H tumors from POLE-exo hypermutator with overlapping signatures.

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Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss of heterozygosity (LOH), large-scale state transitions (LST), and telomeric allelic imbalance (TAI) — with scarHRD, and via the whole-genome HRDetect and CHORD models. Covers the genomic instability score, the PARP-inhibitor clinical context, whole-genome-doubling correction, and the scar-versus-state distinction. Use when computing an HRD score for PARP-inhibitor eligibility, deriving LOH/LST/TAI scars from allele-specific copy number, deciding between scar-based and mutational-signature HRD methods, or interpreting an HRD result in a BRCA-reverted or low-purity tumor.

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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Agent fallback for CEngineServer_GetPlayerNetworkIDString-inlined (auto-generated, category: func). Locate CEngineServer_GetPlayerNetworkIDString 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_GetPlayerNetworkIDString-inlined, CEngineServer_GetPlayerNetworkIDString

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Agent fallback for CEngineGameUI_Shutdown (auto-generated, category: vfunc). Locate CEngineGameUI::Shutdown 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_Shutdown, CEngineGameUI::Shutdown

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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_SetFrameTimeAmnesty (auto-generated, category: vfunc). Locate CEngineServer::SetFrameTimeAmnesty 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_SetFrameTimeAmnesty, CEngineServer::SetFrameTimeAmnesty

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Agent fallback for CEngineClient_ClientCmd_Unrestricted (auto-generated, category: func). Locate CEngineClient_ClientCmd_Unrestricted 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_ClientCmd_Unrestricted, CEngineClient_ClientCmd_Unrestricted

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_GetFrameTimeAmnesty-noinline (auto-generated, category: vfunc). Locate CEngineServer::GetFrameTimeAmnesty 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_GetFrameTimeAmnesty-noinline, CEngineServer::GetFrameTimeAmnesty

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Agent fallback for CEngineServiceMgr_GetEventDispatcher (auto-generated, category: func). Locate CEngineServiceMgr_GetEventDispatcher 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: CEngineServiceMgr_GetEventDispatcher, CEngineServiceMgr_GetEventDispatcher

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Agent fallback for CEngineServer_GetPlayerNetInfo (auto-generated, category: func). Locate CEngineServer_GetPlayerNetInfo 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_GetPlayerNetInfo, CEngineServer_GetPlayerNetInfo

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Agent fallback for CEngineServer_GetSteamUniverse-windows (auto-generated, category: vfunc). Locate CEngineServer::GetSteamUniverse 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_GetSteamUniverse-windows, CEngineServer::GetSteamUniverse

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Agent fallback for CEngineServer_GetSteamUniverse-linux (auto-generated, category: vfunc). Locate CEngineServer::GetSteamUniverse 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_GetSteamUniverse-linux, CEngineServer::GetSteamUniverse

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_GetPlayerInfo-noinline (auto-generated, category: vfunc). Locate CEngineServer::GetPlayerInfo 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_GetPlayerInfo-noinline, CEngineServer::GetPlayerInfo

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_ExecuteClientCmd (auto-generated, category: func). Locate CEngineClient_ExecuteClientCmd 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_ExecuteClientCmd, CEngineClient_ExecuteClientCmd

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_vtable (auto-generated, category: func). Locate CEngineClient_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: CEngineClient_vtable, CEngineClient_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 CEngineServer_IsMapValid-noinline (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-noinline, 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。

Agent fallback for CEngineServer_DumpNetStats (auto-generated, category: vfunc). Locate CEngineServer::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: CEngineServer_DumpNetStats, CEngineServer::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_KickClient (auto-generated, category: vfunc). Locate CEngineServer::KickClient 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_KickClient, CEngineServer::KickClient

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。