Results for “batch”

Python typing exclusion worker: remove assigned mypy exclusion modules in small scoped batches, fix typing issues, run validation, and produce a structured completion summary. Use when running parallel typing-debt workers or when asked to remove modules from pyproject mypy exclusion overrides.

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Audit the health of a PostHog project's data warehouse — find every broken or degraded pipeline item across sources, sync schemas, materialized views, batch exports, and transformations. Use when the user asks "what's broken in my warehouse?", "give me a health check", "audit my data pipeline", "why are some dashboards stale?", or wants a one-shot triage summary before deciding where to spend time. Produces a prioritized report of issues grouped by severity and type, with recommended next steps.

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Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screenshotting. Covers BigWig coverage tracks, BED/peak overlays, gene-model rendering, Hi-C matrix tracks, BedPE link arcs, spike-in-aware normalization, and the bamCoverage --normalizeUsing trap. Use when producing publication figures of genomic loci with stacked aligned tracks (coverage, peaks, genes, interactions) for ChIP-seq, ATAC-seq, RNA-seq, Hi-C, or generic locus visualization.

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Builds diagnostic and prognostic classifiers on omics feature matrices with regularized logistic regression, random forest, and gradient-boosted trees, handling the p>>n regime, batch shortcut learning, class imbalance, and probability calibration. Use when building a classifier from expression, methylation, or variant data, choosing an algorithm for high-dimensional small-n data, or diagnosing a suspiciously perfect AUC. For unbiased evaluation see machine-learning/model-validation; for feature selection see machine-learning/biomarker-discovery; for time-to-event outcomes see machine-learning/survival-analysis.

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Explains ML predictions on omics data with SHAP, LIME, and permutation importance, handling the correlated-feature trap, the conditional-vs-interventional Shapley choice, and the attribution-is-not-causation boundary. Use when interpreting an omics classifier, debugging shortcut/batch learning, or deciding whether an attribution ranking can be trusted as biology. For validated feature selection see machine-learning/biomarker-discovery; explanations are not a selection method.

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Validates predictive models on omics and biomedical data with nested cross-validation, group/batch/temporal-aware splits, the full data-leakage taxonomy, probability calibration, decision-curve net benefit, optimism correction, sample-size planning, and TRIPOD+AI reporting. Use when estimating model performance honestly, choosing a CV scheme, detecting leakage, or judging whether reported discrimination means the model is actually useful. For feature selection itself see machine-learning/biomarker-discovery; for confirmatory-trial inference see clinical-biostatistics/trial-reporting.

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Build AI scientist systems with the ToolUniverse Python SDK for scientific research. Covers the 3 calling patterns (`tu.run` portable dict API, `tu.tools.X` function API, direct class instantiation), tool loading, batch execution, MCP server integration, and embedding-based tool search. Use for SDK programming, custom tool composition, benchmarking pipelines, and integrating ToolUniverse into research workflows.

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Runs and configures curated nf-core community Nextflow pipelines (rnaseq, sarek, atacseq, methylseq, ampliseq, taxprofiler, fetchngs) reproducibly, pinning the pipeline revision with -r and selecting a container engine and institutional config via -profile. Use when deciding to adopt a community pipeline versus author one from scratch; picking a pipeline and pinning its -r revision; selecting -profile test/docker/singularity/conda plus an institutional config from nf-core/configs; building and validating a samplesheet CSV against the pipeline schema (nf-schema); choosing --genome/iGenomes versus custom references; configuring resources and max_memory for SLURM/AWS Batch; using -resume and -stub; and reading MultiQC outputs.

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Analyze metabolomics data end-to-end — metabolite identification, quantification (TIC normalization, batch correction), differential analysis, and pathway interpretation. Use for processing mass-spec metabolomics output, normalization choice, untargeted metabolomics workflows, and integrating with other omics layers.

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Hybrid ML + physics binding affinity prediction. Empirical scoring, MM/GBSA rescoring, multi-method consensus, and batch virtual screening for protein-ligand complexes.

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Promote QA → production by opening a PR from peterdrier/Humans:main to nobodies-collective/Humans:main with a properly-qualified commit summary. Use when the user says "PR to production", "promote to prod", "PR from origin to upstream", "prod PR", or any variation of pushing batched fork changes upstream. Always use this skill for the two-remote promotion flow even if the user doesn't say "prod" explicitly.

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Use when planning a Humans sprint — grooming the backlog into work batches and publishing the Peter-approved subset as a cloud sprint tracking issue. Runs locally with gh access to both repos.

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Inngest イベント駆動 Durable Execution リファレンス。バックグラウンドジョブ、長時間ワークフロー。 createFunction, step.run, step.sleep, step.waitForEvent, step.waitForSignal, step.invoke, step.sendEvent, step.sleepUntil, step.fetch, step.ai.infer, step.ai.wrap, step.metadata, inngest.send, serve, connect, checkpointing, Inngest CLI。 concurrency, throttle, debounce, rate-limit, batching, priority, idempotency, singleton, multi-tenancy フロー制御。 Realtime（channels, topics, publish, subscribe, subscription tokens, useRealtime）、 Agent Evals（scoring, group.experiment）、MCP（Dev Server / Cloud）。 デプロイ先 Next.js, Express, Hono, Cloudflare Workers, Vercel, Netlify, DigitalOcean, Render。

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Claude API (platform.claude.com) の Messages API リファレンス。 streaming (SSE), thinking (adaptive) / preserved thinking / effort, prompt caching, context editing, compaction (on-demand / threshold), structured outputs, Message Batches, token counting, vision / PDF, Files API, citations, embeddings (Voyage AI), errors, rate limits, beta headers, Bedrock / Vertex AI / Foundry 経由アクセス。

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Claude API (platform.claude.com) のモデル・SDK。 model ID・選択基準、Fable・Mythos 5.1 / Opus・Sonnet・Haiku 5.5 移行・破壊的変更、 コスト最適化 (effort / caching / batch / advisor)、pricing、deprecation、用語集。 公式 SDK 7 言語 (Python / TypeScript / Java / Go / Ruby / C# / PHP)、 Claude API 用 CLI `ant` (Claude Code CLI とは別。quickstart / authentication / scripting、`ant apply` resources as code、Managed Agents session 接続)、 middleware、OpenAI SDK 互換、Apple Foundation Models。

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Work on lyrics — the web fallback (LRCLIB, Musixmatch, NetEase, Genius), the in-memory cache, verification, and embedding lyrics into audio file tags. Use this whenever a task touches `services/lyrics.py`, `services/tags.py`, the `/lyrics.json` route, or `scripts/embed_lyrics.py` / `embed_lyrics_cron.sh` — adding or fixing a provider, changing caching/verification, or the batch tagger. Covers the provider contract, the synced-vs-plain rule, the read-only cache, and why writes only ever store plain text.

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Compare cell-type composition and spatial features across conditions in IMC/MIBI cohorts with the patient as the experimental unit, covering pseudoreplication, per-patient aggregation, mixed models, compositional (Dirichlet/scCODA) differential abundance, diffcyt, per-image-to-patient spatial differential testing (SpaceANOVA), batch covariates, and FDR. Use when testing whether a cell type or spatial niche differs between groups, avoiding cell-level pseudoreplication, choosing a differential-abundance method, or correctly powering an IMC cohort comparison.

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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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Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowClean), margin/boundary event removal, signal-drift detection, dead-cell exclusion, CyTOF Gaussian/DNA/event-length checks, instrument calibration/standardization (MESF, CS&T, peak-2), and batch-level outlier flagging. Use when assessing acquisition quality, choosing a cleaning tool, ordering QC relative to compensation, deciding margin removal before density-based steps, or flagging problematic samples before clustering or differential analysis.

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Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.

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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 c_curve / lc_extrap, 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 — see Tips), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for downstream cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for downstream visualisation.

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Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot2 wrappers. Covers MA plot (with the shrunken-LFC compression effect), volcano (with the apeglm caveat that p-values are unchanged), PCA on VST/rlog (never raw counts), sample distance heatmaps, top-DE-gene heatmaps with the row-scaling trap, dispersion / BCV plot interpretation, p-value histogram diagnostics, plotCounts for individual genes, blind=TRUE vs FALSE rationale, and the n=3 visualization stake. Use when generating DE diagnostic plots, choosing VST vs rlog for visualization, troubleshooting suspicious plot patterns (shifted MA cloud, batch-dominated PCA, anti-conservative p-value histogram), or building a standard QC figure panel.

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Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing, apeglm/ashr/normal LFC shrinkage, independent filtering, Cook's outlier handling, VST/rlog transforms, and design formulas including paired, batch, and interaction terms. Use when running bulk DE, choosing DESeq2 over edgeR or limma-voom, building a paired or interaction design, applying LFC shrinkage for ranking or GSEA, choosing Wald vs LRT, troubleshooting padj=NA, picking VST vs rlog, importing salmon/kallisto via tximport, or analyzing prokaryotic RNA-seq.

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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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