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概要と使いどころ
Use when assembling the data and code deposit for an AEJ: Economic Policy manuscript to satisfy the AEA Data and Code Availability Policy and the AEA Data Editor's pre-publication reproducibility check. Builds the openICPSR deposit, README, and restricted-data access paths; it does not run the analysis or write the paper.
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Use when assembling the data, code, and documentation package for an American Economic Journal: Macroeconomics (AEJ: Macro) manuscript to pass the AEA Data and Code Availability Policy and the AEA Data Editor's pre-publication reproducibility check. Covers macro specifics (simulation/calibration code, restricted-access data); it does not write the analysis itself.
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Use when strengthening the reproducibility of an ACM MM (ACM Multimedia) paper or preparing for the ACM MM Reproducibility track and ACM artifact badging — capturing environments, media/data access, seeds, and multimodal pipelines so an independent reviewer can rebuild results and reach Artifacts Evaluated or Results Reproduced badges.
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Use when running the final pre-submission preflight for an Accounting, Organizations and Society (AOS) manuscript — Editorial Manager files (anonymized manuscript, separate title page, declarations), Elsevier policies (competing interests, AI, ethics), and open-access decisions. Checks readiness to submit; it does not handle the post-decision response (aos-rebuttal).
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Use when designing the study for an Accounting, Organizations and Society (AOS) manuscript — qualitative field studies (access, case logic, interviews, observation), behavioral experiments, surveys, historical/archival inquiry, or theory-laden archival designs, each with the ethics and site-anonymity groundwork done early. Designs the inquiry; it does not run the coding or estimation (aos-data-analysis).
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Use when strengthening an AAAI paper's reproducibility checklist (placed after references), experimental traceability, seed and hyperparameter reporting, compute and cost disclosure, dataset access and licensing, code/data ZIP readiness, and the claim-to-evidence map that Phase-1 reviewers use to judge rigor across AAAI's broad AI scope.
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Use when preparing an accepted AAMAS paper for the IFAAMAS open-access camera-ready, covering author de-anonymization, proceedings metadata, two-column reflow of game figures and learning curves, resolving rebuttal-stage promises, registration, in-person presentation, and the public code and environment release for a multiagent paper.
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Use when responding to an Academy of Management Annals (Annals) proposal decision or full-review referee letter — framework/attitude asks, coverage gaps, balance complaints, and accessibility. Drafts the response letter and revision plan; it does not run the portal preflight (amann-submission) or redesign the framework from scratch (amann-organizing-framework).
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。
Full video production sequence with script review, actual ingredient choices, controlled generation, editing, evidence-based quality review, polish, captions and delivery. A host binding supplies project storage, authentic approvals, provider access and billing.
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Database access patterns for performance. Separate read/write models, avoid N+1 queries, use AsNoTracking, apply row limits, and never do application-side joins. Works with EF Core and Dapper.
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Extracts cfDNA fragmentomics features (DELFI genome-wide short/long ratios, WPS nucleosome positioning, Griffin GC-corrected accessibility profiles, end-motifs/MDS, OCF) for cancer detection and tissue-of-origin from plasma WGS. Centers on the nuclease-footprint reframe (every feature re-reads one nucleosome object), the mandatory GC correction, and the cross-protocol non-comparability that breaks naive classifiers. Runs FinaleToolkit (real CLI/Python, MIT) and the Griffin Snakemake pipeline; DELFI is a method, not a package. Use when deriving fragment-based signal from cfDNA, choosing a feature family for detection vs subtyping, or diagnosing why a fragmentomic model failed validation.
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Build enhancer-driven gene regulatory networks (eGRNs) by integrating single-cell RNA-seq and ATAC-seq using SCENIC+, CellOracle base GRNs, Pando, FigR, DIRECT-NET, TRIPOD, and scMEGA. Covers the accessibility-defines-enhancers principle, peak-to-gene linking and its cell-composition confound, the paired-vs-unpaired decision, and TF-region-gene eRegulon triplets. Use when analyzing 10x multiome or paired/unpaired scRNA+scATAC to infer cis-regulatory GRNs. For RNA-only regulons see scenic-regulons; for in silico TF perturbation see perturbation-simulation.
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Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces assembly_summary.txt scraping and many EFetch workflows). Use when bulk-pulling genome assemblies, gene metadata across species, ortholog sets, or BLAST databases; when E-utilities are too slow for genome-scale work; or when automatic checksum verification, parallel download, and clean accession-driven retrieval are required. Encodes the JSON-lines output format, dataformat conversion, --dehydrated for cloud workflows, and when Datasets is/isn't the right tool.
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Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON schema, choosing between UniProtKB/UniRef/UniParc/Proteomes resources, deciding stream vs search endpoint for batch retrieval, running ID-mapping jobs with the async pattern, handling isoform suffixes, or filtering reviewed Swiss-Prot vs auto-annotated TrEMBL. Encodes the legacy URL migration (2022), the new JSON schema layout, and bulk-pull patterns.
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Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.
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Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.
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Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.
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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.
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Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing per-cell QC, choosing between ArchR/Signac/SnapATAC2 ecosystems, building per-cluster consensus peaksets, integrating with paired scRNA-seq, doublet detection (AMULET vs ArchR vs scDblFinder), or running pseudobulk differential accessibility per cluster.
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Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
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Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target genes, choosing between contact-aware (ABC, ENCODE-rE2G), accessibility-only (Cicero), and orthogonal (HiChIP H3K27ac, EpiMap) approaches, validating predictions against CRISPRi-FlowFISH gold-standard, or building cell-type-specific regulatory maps for fine-mapping or therapeutic target discovery.
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Use when the user mentions simulator testing, visual verification, push notification testing, location simulation, screenshot capture, OR live accessibility validation (VoiceOver announcements, Dynamic Type, ADA checks) on the simulator.
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Use when asking about Axiom skills or axbuild build/test capture, xclog console, xcsym .ips/MetricKit/.crash symbolication, xcui simulator UI/accessibility, or xcprof xctrace/CPU profiles.
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Use when work crosses into Apple's system surfaces rather than your own UI or data — Siri and Shortcuts, widgets, Live Activities, in-app purchase, localization, privacy prompts, alarms, timers, calendar, reminders, contacts, SharePlay, VoIP and CallKit, accessory pairing, weather, Spotlight indexing, background tasks, Background Assets, push, or push on networks with no internet.
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。