127 件 ・ 関連度順
概要と使いどころ
Advises on setting up and validating topic models for survey and experimental text: discovery vs. measurement, STM/LDA/BERTopic choice, preprocessing, covariate formulas, choosing K across coherence, FREX, held-out likelihood, and residuals, validating topics against human coding, robustness, and reporting. Coding against a fixed codebook goes to text-classification.
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。
Create video compositions, animations, title cards, overlays, captions, voiceovers, audio-reactive visuals, and scene transitions in HyperFrames HTML. Use when asked to build any HTML-based video content, add captions or subtitles synced to audio, generate text-to-speech narration, create audio-reactive animation (beat sync, glow, pulse driven by music), add animated text highlighting (marker sweeps, hand-drawn circles, burst lines, scribble, sketchout), or add transitions between scenes (crossfades, wipes, reveals, shader transitions). Covers composition authoring, timing, media, and the full video production workflow. For dev-loop CLI commands (init, lint, inspect, preview, render) see the hyperframes-cli skill; for asset preprocessing commands (tts, transcribe, remove-background) see the hyperframes-media skill.
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。
Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF), and parses FlowJo/Cytobank/Diva workspaces. Covers FCS 2.0/3.0/3.1/3.2 internals ($PnE linear-vs-log, $DATATYPE, $SPILLOVER vs SPILL vs $COMP, $TIMESTEP), channel/parameter metadata, the silent linearize/truncate defaults, and R (flowCore, flowWorkspace, CytoML) plus Python (FlowKit, readfcs) readers. Use when loading flow or mass cytometry data, mapping detector channels to antibodies, extracting the event matrix, choosing a reader, or bridging FCS to the scanpy/AnnData ecosystem before preprocessing.
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。
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, 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), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for visualisation.
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。
Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.
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。
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.
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。
Decompose DAGs into execution chains using width bounds, stratification, virtual nodes, and matching. Use when minimizing workflow lanes in dependency graphs. NOT for cyclic graphs, generic scheduling, or one-off queries with no preprocessing payoff.
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。
fMRI data analysis — preprocessing, GLM modeling, and group-level inference for task and resting-state studies.
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。
EEG preprocessing and analysis — filtering, artifact removal, time-frequency decomposition, and ERP workflows.
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。
Analyze text data with NLP — preprocessing, embeddings, topic modeling, sentiment, classification, and evaluation. Use when turning unstructured text into structured insight.
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。
Manage ML datasets with the datasets ecosystem — loading, streaming, preprocessing, versioning, and sharing. Use when data handling (not modeling) is the bottleneck.
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。
Analyzing behavioral experiment data — RT/accuracy preprocessing, mixed-effects models, and robust inference.
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。
Scalable data processing for ML workloads. Streaming execution across CPU/GPU, supports Parquet/CSV/JSON/images. Integrates with Ray Train, PyTorch, TensorFlow. Scales from single machine to 100s of nodes. Use for batch inference, data preprocessing, multi-modal data loading, or distributed ETL pipelines.
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。
End-to-end small RNA-seq analysis from FASTQ to differential miRNA expression and target prediction. Use when analyzing miRNA, isomiR, tRF, or piRNA sequencing data through preprocessing, quantification, discovery, DE, and targets.
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。
End-to-end spatial transcriptomics workflow for Visium/Xenium data. Covers data loading, preprocessing, spatial analysis, domain detection, and visualization with Squidpy. Use when analyzing spatial transcriptomics data.
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。
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
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。
Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware alignment (NO deduplication for non-UMI MeRIP), deepTools replicate-concordance + IP-enrichment QC, PreSeq saturation curves, exomePeak2 (transcript-aware Poisson GLM) peak calling, optional MACS3 broad-peak cross-check, DRACH motif confirmation as a sanity check (NOT a per-peak filter), exomePeak2 differential calling via the four-BAM-vector interface (bam_ip + bam_input control; bam_treated_ip + bam_treated_input treatment), ChIPseeker annotation, and the canonical Guitar metagene with stop-codon enrichment as the biological QC anchor. Use when running a complete MeRIP analysis from raw reads, when chaining the constituent epitranscriptomics skills (merip-preprocessing -> m6a-peak-calling -> m6a-differential -> modification-visualization), or when wrapping the pipeline in Snakemake / Nextflow.
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。
End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statistics. Use when analyzing imaging mass cytometry data end-to-end.
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。
Designs and analyzes stable-isotope-resolved metabolomics (SIRM / isotope tracing / fluxomics) experiments that measure metabolic ACTIVITY via 13C/15N/2H tracers, distinct from steady-state pool profiling. Covers tracer choice, isotopologue vs isotopomer, mass-isotopomer distributions (MID), fractional enrichment, the mandatory natural-abundance + tracer-purity correction (IsoCor, AccuCor), and the metabolic/isotopic steady-state vs non-stationary (INST-MFA) distinction. Use when feeding a labeled tracer and interpreting labeling patterns, correcting raw isotopologue intensities, computing or plotting an MID, or deciding tracing vs abundance profiling. For absolute pool concentration and MRM mechanics see metabolomics/targeted-analysis; for constraint-based genome-scale flux (FBA, not empirical tracing) see systems-biology/flux-balance-analysis; for feature detection see metabolomics/xcms-preprocessing; for pathway enrichment that ignores the pool-vs-flux caveat see metabolomics/pathway-mapping.
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。
Designs and validates quantitative targeted metabolomics assays (MRM/SRM on triple-quadrupole, PRM on high-resolution instruments) to report absolute concentrations. Covers the internal-standard strategy (external cal -> global IS -> standard addition -> stable-isotope-labeled IS), weighted calibration judged by back-calculated %RE not R-squared, ion-ratio quantifier/qualifier confirmation, matrix-effect/recovery characterization, and ICH M10 method validation. Use when quantifying a closed panel of known metabolites with units, building or validating an LC-MS/MS assay, choosing an IS or calibration weighting, or judging whether a reported concentration is trustworthy. For untargeted feature detection see metabolomics/xcms-preprocessing; for group statistics see metabolomics/statistical-analysis; for flux/MID/tracing see metabolomics/isotope-tracing.
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。
Inventory staged local EcoSIM data at project startup and validate input readiness for a selected site, simulation period, and preprocessing or analysis workflow. Use before data-dependent work or when relevant inputs change.
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。
Download Copernicus CDS ERA5 single-level point time-series climate forcing for non-US or non-NLDAS EcoSIM sites from longitude/latitude coordinates. Use when a paper-derived site is outside the NLDAS domain, lacks AmeriFlux/FLUXNET curated forcing, or needs global ERA5 variables such as 2m temperature, dewpoint temperature, surface pressure, solar radiation, precipitation, and 10m wind components for EcoSIM preprocessing.
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。
Download NASA GES DISC NLDAS_FORA0125_H version 2.0 primary hourly forcing data for a point location. Use when Codex needs to retrieve NLDAS File A meteorological forcing from the GES DISC API or HTTPS archive for a longitude/latitude pair, including Earthdata username/password authentication, hourly URL generation, nearest-grid-point extraction, CSV output, or EcoSIM climate-forcing preprocessing.
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。
Load and preprocess imaging mass cytometry (IMC) and MIBI data from raw MCD/TXT through hot-pixel removal, spillover compensation, and variance-stabilizing transformation, covering readimc/steinbock ingestion, NNLS spillover compensation (CATALYST), IMC-Denoise, and the IMC arcsinh-cofactor question. Use when starting analysis from raw MCD files, building per-channel TIFF stacks, compensating channel spillover, choosing an arcsinh cofactor, or preparing single-cell intensities for phenotyping.
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。