359 件 ・ 関連度順
概要と使いどころ
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream analysis. Use when assessing ChIP-seq data quality metrics.
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给一个主题，产出一条黑底 MG 风格（幕底可选星点或点阵波）、有配音字幕章节进度条的科普讲解视频（中文或英文；Remotion 代码动画；时长由用户定，常用 3–5 分钟）。内含可编译模板、图元库、配音/分镜/渲染工具、风格与动效规范、多 agent 分工协议与 QC 判据，以及一条完整样片（《RAG 与知识库》）作为质量标尺。Turn any topic into a narrated motion-graphics explainer video in Chinese or English, on a black canvas with a star-field or dot-field backdrop, TTS voiceover, subtitles and a chapter progress bar, every frame drawn in code with Remotion. Use when the user asks for an explainer, educational or science-communication video about a topic, or wants an article or document turned into a video.
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Use when correcting batch effects in merged bulk expression matrices with sample-level batch metadata while preserving biological group structure and generating before-and-after QC plots. NOT for: single-cell integration, raw FASTQ processing, differential expression without batch labels, or datasets without biological groups.
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Analyze, recreate, align, and verify reference-video motion. Use when the user asks to recreate, copy, match, align, pixel-align, or compare a video; when a HyperFrames or Remotion remake is judged not aligned; when fixed reference playback and reusable motion components must be separated; or when delivery needs full-frame runtime, render, decode, boundary, timing, and archive evidence instead of sampled screenshots alone.
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Render, preview, validate, and burn consistent production subtitles from QC-passed real-timestamp caption artifacts. Use for AI-video production, washed-video production, IndexTTS2 explainers, practical long-form videos, talking-head edits, Kimi-style dark rounded captions, warm-white translucent captions, subtitle styling, subtitle overlays, or fixing caption size, position, shadow, drift, and 4K scaling. Always pair with ra-audio-to-subtitles when final word timestamps do not already exist.
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Analyze a public or local reference video, isolate a time range, deconstruct its layout, motion, timing, and transitions, then build an original verified motion replica with reusable templates and final MP4 QC. Use when the user says 复刻这个视频效果, 参考这个视频做同款动效, 拆解前 N 秒, 还原方框/连线/卡片动画, or provides a video or URL as a motion reference rather than asking to copy its footage or script.
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Motion-first AI video director for topic-to-video creation. Use when the user gives a theme, idea, article, script, or brief and wants AI to freely create a real animated video instead of a PPT/slideshow-style explainer; when deciding visual metaphors, motion grammar, scene beats, component choices, generated image needs, HyperFrames/Remotion implementation strategy, and anti-PPT QC.
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Create and composite HeyGen digital-human videos in the content workspace. Use whenever the user asks for a 数字人, 数字人5, HeyGen, AI 口播人物, 数字人小窗, 圆形头像口播, full-screen digital human, or asks to make a video that uses the existing avatar. Enforce Creator-plan CLI OAuth, the configured Digital Twin, local IndexTTS2 narration, Avatar III for an unspecified digital human but Avatar V whenever the named preset 数字人5 is requested, adaptive face measurement plus the approved human-reviewed visual-centering offset in the headroom_08 circular bottom-left layout unless full-screen is explicitly requested, subtitle-safe placement, credit-aware master reuse, final QC/archive routing, and mandatory pairing with `heygen-avatar-motion` before any motion prompt or paid generation.
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Create dark cinematic SaaS/product motion videos in the Presenton-like "magic UI" style: black starfield stage, bottom purple glow, large kinetic type, cyan-to-magenta CTA buttons, prompt cards, floating UI templates, integration badges, model rings, export objects, speed-blur transitions, and short product capability arcs. Use when the user asks for "这种风格", "同款风格", dark SaaS promo, AI product demo, magic UI product video, or a style-level creation inspired by a reference video. Do not use for pixel-level or frame-accurate replication; use rn-replica-qc first for that.
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End-to-end video production orchestration for the content-creation workspace. Use when the user asks to make, recreate, package, render, QC, or archive a video; when the user says 制作待制作队列, 按交接稿制作, 制作队列视频, or points at a handoff project folder under 01-内容生产/视频工作台/待制作/ (contract file 交接稿.md inside) or an image-card handoff under 01-内容生产/图文工作台/待制作/ (its frontmatter is the binding production contract); when a request could route to HyperFrames, Remotion, captions, TTS, download/transcription, website/product videos, motion graphics, or reference replication; or when the user needs production planning before editing.
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Final QC gate for a rendered 9:16 video ad, run before it is published. One script checks what a machine can decide — exact 1080x1920 size, a hook that moves and speaks in the first second, no frozen stretches, no dead air, no black frames, the brand's real logo on the end card (never a favicon, never a redrawn or wrong logo), end-card colours near the brand palette — and builds one contact sheet (frames with the TikTok/Reels UI safe zones shaded, beside the logo, product images and a font specimen) for the checks that need eyes — font, product likeness, product consistency across scenes, safe zones. A declared silent-text profile covers silent, text-led formats such as kinetic text (no audio track needed, short blank beats between text beats allowed within fixed bounds). Exit 0 PASS / 2 FAIL / 3 ERROR. Use on every finished video master before pinning it.
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QC gate for a generated static ad image — verify the file opens, matches the requested dimensions, shows the correct product/subject (right shape, colour, label, logo), and has no garbled text or severe artifacts. Records pass/fail/needs-human in verification.md. Used as the final check in the static ad remix flow before shipping.
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Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap spacers (adds no sequence). Covers Hi-C/Omni-C scaffolding (YaHS, SALSA2, 3D-DNA/Juicer), Hi-C read-mapping prerequisites (map each end separately, no mate rescue, dedup, enzyme-aware), reading the contact map for misjoins/inversions/false-duplications, manual curation in Juicebox/PretextView (the VGP/DToL standard), reference-guided scaffolding (RagTag) and its karyotype-erasure hazard, genetic-map (ALLMAPS) and Bionano optical-map integration, chimera-breaking before scaffolding, gap-filling, and telomere/contig-vs-scaffold-N50 QC (tidk). Use when turning contigs into chromosomes with Hi-C, integrating a linkage map or optical map, choosing a scaffolder by available linking data, or judging whether a chromosome-scale assembly is trustworthy.
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Quality control for IMC/MIBI data across pixel, channel, image, slide, and batch levels, covering Poisson-count SNR (cell-level Gaussian-mixture and empty-channel comparison), spillover-matrix QC (the three physical sources), drift and the missing EQ-bead analog, acquisition artifacts, and sample-of-origin batch effects. Use when deciding whether to keep or drop a channel, ROI, or slide, distinguishing a dim antibody from a failed one, reading a spillover matrix, or diagnosing batch-driven clustering before analysis.
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Treats a ctDNA assay as a molecule-counting experiment at the Poisson edge and builds its analytical-validation case the measurement-science way. Covers the genome-equivalent currency (~330 haploid copies/ng), the lambda = input_GE x VAF sampling ceiling (lambda>=3 for ~95% detection), the error-suppression ladder (raw NGS ~1e-3 -> single-strand UMI ~1e-4/1e-5 -> duplex <1e-7), the CLSI EP17 LoB/LoD/LoD95/LoQ framework, the per-locus-vs-panel-integrated LoD distinction that lets bespoke MRD reach ppm, contrived/SEQC2 reference standards, and honest LoD reporting conditioned on input mass + consensus depth + replicate detection rate. Use when stating or trusting a sensitivity claim, designing a dilution-series validation, deciding how many genome equivalents are needed at a target VAF, choosing a single-locus vs panel-integrated LoD, or auditing a "detects 0.1% VAF" claim.
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Computes and interprets sequencing read depth and coverage over a genome, windows, or target regions with mosdepth (windowed depth, cumulative distribution, --quantize callable BEDs), bedtools genomecov/coverage (bedGraph tracks, per-target stats), samtools depth/coverage (per-base depth, per-contig depth+breadth). Covers the breadth-vs-mean distinction, the cumulative-coverage curve, evenness (CV/Fano/fold-80/Gini), what each tool silently counts (duplicates, secondary/supplementary, MAPQ, read span vs fragment, mate-overlap), the samtools-depth 8000-cap version trap, and the bedtools coverage -a/-b orientation flip. Use when assessing sequencing adequacy, building coverage tracks, computing breadth at a depth threshold, defining callable regions, or QCing target-capture uniformity.
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Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.
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Assembles microbial-community sequencing into metagenome-assembled genomes (MAGs) with metaFlye (ONT), metaSPAdes/MEGAHIT (Illumina), and hifiasm-meta/metaMDBG (PacBio HiFi), then recovers genomes via multi-binner consolidation (MetaBAT2, MaxBin2, CONCOCT, SemiBin2, VAMB -> DAS_Tool) and QCs them against MIMAG with CheckM2, GUNC, and GTDB-Tk. Covers why a metagenome is not a genome (uneven coverage, micro-diversity, strain collapse to consensus), differential-coverage binning, co-assembly vs per-sample, the rRNA-operon collapse that fails short-read MAGs, and strain resolution with inStrain. Use when reconstructing genomes from a microbiome, soil, ocean, or gut community, recovering MAGs, or resolving strain-level variation.
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Estimates time-scaled phylogenies, molecular-clock rates, effective reproduction number R_e, and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict/relaxed clocks; coalescent, Bayesian-Skyline, Skygrid, Birth-Death-Skyline, and sampled-ancestor priors; structured coalescent via MASCOT). Covers root-to-tip clock QC via TempEst, date-randomisation tests, recombination masking via Gubbins/ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction, multi-chain convergence diagnostics, and reconciling phylodynamic R_e with case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline models, diagnosing temporal-signal failure, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.
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Assigns pathogen lineages (SARS-CoV-2 Pangolin UShER mode; Nextclade clade + QC; pango-designation alias resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage-fitness modelling (multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data and Nextclade dataset version pinning (mandatory; lineage-defining mutations change with dataset), Freyja barcode forward-only date constraint, ARTIC primer scheme churn (V3/V4/V4.1/V5.3.2/Midnight) with dropout regions, and recombinant X-prefix designation lag. Use when assigning Pango lineages and Nextclade clades to viral consensus sequences, building Nextstrain Augur surveillance pipelines, deconvolving wastewater into lineage frequencies with Freyja, tracking lineage frequencies over time, handling ARTIC primer dropouts, or running surveillance for SARS-CoV-2/influenza/Mpox/RSV/H5N1/measles.
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Assembles haplotype-resolved diploid and telomere-to-telomere (T2T) genomes from PacBio HiFi reads with hifiasm (HiFi-only, Hi-C, or trio phasing) and verkko (HiFi + ultralong ONT for T2T), extracting contigs from GFA and routing phasing QC to k-mer/trio metrics. Covers why a primary assembly is a haplotype mosaic that exists in no cell, partial-vs-full phasing (the .bp. vs .dip. filename convention), the purge-default trap on inbred samples, the --hom-cov coverage-estimate alarm, and verkko-vs-hifiasm for T2T. Use when assembling a diploid eukaryote from HiFi, phasing haplotypes with parents (trio) or Hi-C, deciding whether to chase T2T, or diagnosing switch errors invisible to N50/BUSCO/QV.
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Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and correctness (reference-free Merqury QV, Inspector/CRAQ structural errors, asmgene false-duplication/collapse). Covers why N50 is the most-gamed metric, why QV measured on the polishing reads is circular, distinguishing uncollapsed haplotigs from real WGD, and the EBP/VGP 6.C.Q40 standard. Use when judging whether an assembly is good enough to annotate or publish, comparing assemblers, diagnosing a fragmented or duplicated assembly, or assessing a phased diploid assembly.
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Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).
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Designs pooled sgRNA libraries for CRISPR knockout, interference (CRISPRi), activation (CRISPRa), Cas12a multiplex, base-editor, and prime-editor screens. Covers on-target scoring (Rule Set 2, Azimuth, DeepSpCas9, CRISPRon), off-target scoring (CFD, MIT), TSS-relative positioning for CRISPRi/a (Horlbeck, Dolcetto, Calabrese), PAM-variant chemistries, control-guide composition, oligo cloning architecture, and library QC. Use when choosing a genome-wide library (GeCKOv2 vs Avana vs Brunello vs TKOv3 vs Inzolia), designing a focused or paralog-focused custom library, picking CRISPRi vs CRISPRa TSS windows, deciding control-guide proportions, or diagnosing library skew and dropout in a freshly cloned pool.
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