173건 · 관련도순
Use when assembling the data and code replication package for an American Economic Journal: Applied Economics (AEJ: Applied) manuscript to pass the AEA Data and Code Availability Policy and the AEA Data Editor's pre-publication reproducibility check. Builds the openICPSR deposit and README; it does not run the analysis or write the paper.
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Use when packaging code, models, datasets, or media as ACM MM (ACM Multimedia) artifacts — building the anonymous review package versus the public release, and choosing between the Open Source Software Competition, the Dataset track, the Reproducibility track, and main-track supplementary evidence, each with its own blinding and expectations.
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Use when auditing an ACM MM (ACM Multimedia) submission for OpenReview readiness — thematic-area choice, the 6-8 page ACM sigconf budget, references-only overflow, double-blind anonymity versus the single-blind Reproducibility/Open-Source/Dataset tracks, supplementary media, dual submission, desk-reject triggers, and last-week sequencing.
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Use when preparing the ACM MM (ACM Multimedia) camera-ready version of record — de-anonymizing safely, completing the ACM rights form and CCS concepts, meeting ACM sigconf requirements, releasing code/data/media artifacts and any earned reproducibility badge, registering, and planning the oral/poster presentation in Rio.
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当你为《电子学报》(Acta Electronica Sinica, AES) 稿件强化可复现性与实验可重复时使用。覆盖电子/信息/信号处理/通信类工作的实验环境记录、随机性控制、数据与预处理透明、算法伪代码与超参数完整披露、硬件与仿真工具链版本、统计显著性与多次运行、以及在中文学报正文与附录里如何组织可复现信息。帮助作者用可复现性作为通过《电子学报》外审、抵御"结果无法重复"质疑的核心竞争力，而非事后补救。
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当你在为《自动化学报》(Acta Automatica Sinica, AAS) 提升实验可复现性、组织复现包、防范数据污染时调用。覆盖环境与依赖固定、随机种子与多次运行、数据划分与防泄露、控制仿真的求解器/步长/系统参数记录、超参数与调参协议披露、以及配合双盲的匿名化复现材料，帮助控制/自动化/模式识别方向的中文稿在 Acta Automatica Sinica 外审中经得起"结果能否复现"的追问。
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Use when packaging AAAI code, data, multimedia appendices, technical appendices, reproducibility evidence, and post-acceptance artifact releases without violating double-blind or immutable-supplement rules.
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Use when revising an AAAI manuscript for broad-AI-audience fit, a first-page contribution statement legible to non-specialist Phase-1 reviewers, two-column readability, concise novelty claims, reproducibility-checklist alignment, hedged limitations and ethics, and policy-aware framing of AI-system and capability claims.
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Use when auditing an AAAI main technical track submission for OpenReview readiness, double-blind anonymity, page limits, reproducibility checklist, supplementary material, author limits, multiple-submission policy, and AAAI AI-use policy compliance.
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Use when designing or auditing AAAI experiments for the broad-AI program committee, including baselines, ablations, statistical significance, robustness, human evaluation, AI-for-Social-Impact and alignment/safety evidence, compute and cost reporting, and reproducibility-checklist alignment for Phase-1 survival.
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Compares Hi-C contact maps between conditions across the right scale -- differential bin-pair contacts (multiHiCcompare, diffHic), differential A/B compartments (dcHiC), differential TAD boundaries (delta insulation), and differential loops (diffloop, DiffHiChIP) -- with distance-stratified between-sample normalization, replicate-aware NB-GLM FDR, HiCRep SCC reproducibility gating, and CNV correction for cancer/aneuploid samples. Use when comparing Hi-C between treatment and control, finding differential contacts/compartments/boundaries/loops, normalizing two maps of unequal depth, choosing a replicate-aware test, gating replicates with SCC, or correcting copy-number artifacts before a tumor-vs-normal comparison.
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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.
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Controls error rates across thousands of simultaneous tests in genomics discovery using false-discovery-rate methods (Benjamini-Hochberg 1995; Benjamini-Yekutieli 2001 for arbitrary dependence; Storey q-value with pi0 estimation; local FDR; independent filtering Bourgon 2010; covariate-weighted FDR via IHW Ignatiadis 2016), plus family-wise error control (Bonferroni, Holm) and the GWAS genome-wide threshold. Covers the FDR-versus-FWER choice as the discovery-versus-confirmatory distinction, the dependence assumptions behind BH (PRDS) versus BY, pi0 estimation, the independent-filtering and false-coverage-rate traps, and reproducibility ranking via IDR (Li 2011). Use when correcting p-values from genome-wide tests, choosing between BH/BY/q-value/Bonferroni, setting an FDR threshold, applying IHW or independent filtering, or interpreting q-values. For confirmatory trials with few pre-specified endpoints (closed testing, graphical/gatekeeping), see clinical-biostatistics/multiplicity-graphical.
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Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST. Encodes Ensembl version stripping with GENCODE _PAR_Y preservation, the Ziemann 2016 Excel autocorrect debacle and Bruford 2020 HGNC renames (SEPT*->SEPTIN*, MARCH*->MARCHF*, MARC*->MTARC*, DEC1->DELEC1), OCT4/POU5F1 alias resolution, biomaRt archive endpoints for release pinning, the `filters` (plural) gotcha, MANE Select for clinical reporting, cross-species orthology via Ensembl Compara / OMA / OrthoDB, and tx2gene construction for tximport. Use when converting gene IDs across systems, handling renamed symbols, building tx2gene, pinning to a specific Ensembl release for reproducibility, or mapping cross-species orthologs.
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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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Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity (preseq), FRiP, IDR replicate reproducibility, read-distribution metagene, SMInput vs IgG control rationale, rRNA / snoRNA contamination, fragment-length distribution, and ENCODE-compliance thresholds. Use when assessing whether a CLIP library passed, deciding lenient vs stringent peak thresholds, comparing replicates with IDR rescue and self-consistency ratios, or distinguishing failed IP from over-amplified library.
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Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases simultaneously without managing per-source APIs, and when reproducibility-grade analyses require recording source data versions via _meta.
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Review and revise academic papers with a senior-reviewer workflow. Use when an AI research/coding agent needs to work on an existing paper draft, PDF, LaTeX project, Word document, markdown manuscript, rejected paper, or paper idea that already has a concrete direction, and produce: paper maps, weakness audits, insight/novelty checks, reviewer objections, claim-experiment matrices, theory/proof checks, experiment plans, statistics/reproducibility audits, figure/table audits, ethics/compliance checks, revision plans, detailed section edits, or final submission checklists.
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Structured, reproducible analysis documentation. Use when documenting analysis findings, creating analysis notebooks, ensuring reproducibility, or building analysis archives for future reference.
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Use when you need framework-agnostic Docker and container image guidance for Java projects - Dockerfile design, multi-stage Maven builds, jlink custom runtimes, micro runtime distributions such as Alpaquita, JVM container ergonomics, non-root execution, image metadata, .dockerignore, reproducible builds, vulnerability scanning, SBOM awareness, and production-safe container defaults. This should trigger for requests such as Review Java Dockerfile; Improve Docker image security; Add jlink runtime to a Java container; Add containerization to a Java project; Optimize Java container image size; Review Docker build reproducibility. Part of Plinth Toolkit
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Use when the user wants to prepare code for open-source release, create reproducible research artifacts, or structure a repository for publication. Triggers on phrases like "publish code", "open source release", "reproducibility", "research repository", "code release", or "prepare for publication".
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Check a mathematical-modeling paper's in-text citations, bibliography, appendix length and content, code, supporting files, reproducibility, consistency, and anonymity. Use when the user provides a paper or related materials and wants one consolidated P0-P3 audit; do not generate or invent missing sources or programs.
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Evaluating scientific evidence and claims. Covers study design hierarchy (RCT to expert opinion), effect sizes (OR, RR, NNT, Cohen's d), confounding, p-value vs clinical significance, GRADE quality assessment, reproducibility, and bias types (selection, information, confounding, reporting). Use when reading a paper or assessing claims.
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Structured peer review of manuscripts and grants. 7-stage evaluation: initial assessment, section review, statistical rigor, reproducibility, figure integrity, ethics, writing. Covers CONSORT/STROBE/PRISMA and report structure. For evidence quality see scientific-critical-thinking; scoring see scholar-evaluation.
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