2,309 件 ・ 関連度順
概要と使いどころ
Unified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold, Enrichr enrichment, OpenTargets disease/drug, CELLxGENE single-cell, cBioPortal/COSMIC cancer, ARCHS4 expression. Spans genomics, proteomics, disease. For batch/advanced BLAST use biopython; for multi-DB Python SDK use bioservices.
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Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via majority voting. Outputs per-method labels, consensus, agreement score. Use when single-method annotation is insufficient or you need ensemble uncertainty for novel states.
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Cell type annotation strategy for scRNA-seq: name clusters manually from canonical markers, transfer labels from a reference (CellTypist, popV), or do both and validate one against the other. Covers matching tissue and developmental stage, marker evidence, annotation confidence, doublets, unresolved clusters. Use when planning or troubleshooting how to annotate cells.
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Unified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI. For deep single-DB queries use dedicated tools (gget for Ensembl, pubchempy for PubChem); bioservices excels at cross-database workflows.
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Aggregates QC from 150+ bioinformatics tools into one interactive HTML report. Scans FastQC, samtools, STAR, HISAT2, Trim Galore, featureCounts, Kallisto, Salmon, Picard, GATK logs; merges per-sample stats with plots. For NGS pipeline-wide QC. Use FastQC directly for single-sample; MultiQC for multi-sample reporting.
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Annotated matrices for single-cell genomics. Stores X with obs/var metadata, layers, embeddings (obsm/varm), graphs (obsp/varp), uns. Use for .h5ad/.zarr I/O, concatenation, scverse integration. For analysis use scanpy; for probabilistic models use scvi-tools.
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Genomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest features. Core for ChIP-seq peak annotation, region filtering, genome arithmetic. Use tabix for indexed single-region queries; use deeptools for normalized bigWig coverage.
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Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLURM/SGE), cloud (AWS/GCP/Azure), or Kubernetes via a single config change. Powers nf-core. Use Snakemake for rule-based Python workflows; use Nextflow for containerized, cloud-native, and nf-core pipelines.
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Parallel/distributed computing for larger-than-RAM data. Components: DataFrames (parallel pandas), Arrays (parallel NumPy), Bags, Futures, Schedulers. Scales laptop to HPC cluster. For single-machine speed use polars; for out-of-core without cluster use vaex.
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Filter degenerate, uninformative inputs before statistical tests: single-sequence alignments, empty files, constant features, zero-variance inputs, all-NaN columns. See nan-safe-correlation for NaN-aware correlation; statistical-analysis for test guidance.
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GRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest). Load matrix, filter by TFs, infer TF-target-importance links, save network. Dask-parallelized to single-cell scale. Core SCENIC component.
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Python library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm. Locate particles (fluorescent spots, colloids, vesicles, cells) per frame, link into trajectories, filter short tracks, and compute MSD for diffusion analysis. 2D/3D with subpixel accuracy; reads TIF stacks, AVI, image series via pims. Use for quantitative SPT and diffusion coefficient extraction from fluorescence or brightfield video.
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omics-plotting: publication-style figure authoring for omics / bioinformatics results with matplotlib / seaborn. Read this before writing any plotting or figure code in any omics analysis — RNA-seq, proteomics, single-cell, variant, or database results — not only when a plot is explicitly requested: whenever an analysis will produce a figure, load this first and follow its recipes. Covers volcano, MA, expression / correlation heatmap, GSEA bar / dot plot, box / violin / bar / ridgeline, PCA / UMAP / t-SNE scatter, Kaplan–Meier, Manhattan / QQ / forest. Supplies a shared journal-ready style and copy-paste recipes so every figure looks like one consistent system. To combine several plots into ONE multi-panel composite figure, use the sibling `multipanel` skill.
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Orchestrate multi-agent swarms with agentic-flow for parallel task execution, dynamic topology, and intelligent coordination. Use when scaling beyond single agents, implementing complex workflows, or building distributed AI systems.
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Remove the discourse-level (structural) signs of AI writing that survive surface editing: stated lessons and moral-of-the-story closers, tidy single-track arcs, embodied-emotion performance ("chest tightened"), vague allusions instead of named references, unbroken linear structure, and shape convergence across pieces. Grounded in the StoryScope study (Russell et al. 2026): narrative structure alone detects AI text at 93.2% F1, and professional stylistic rewriting moved detection only 1.6 points. Use as the SECOND pass after the humanizer skill (which handles words and phrasing) whenever writing or revising LinkedIn posts, course lessons, blog posts, essays, newsletters, or emails that must read as human. Triggers: "humanize", "de-slop", "AI tells", "make this sound human", "structural pass", "deep humanize".
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Provides parameterized testing patterns with JUnit 5, generates data-driven unit tests using @ParameterizedTest, @ValueSource, @CsvSource, @MethodSource. Creates tests that run the same logic with multiple input values. Use when writing data-driven Java tests, multiple test cases from single method, or boundary value analysis.
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Provides TypeScript patterns for DynamoDB-Toolbox v2 including schema/table/entity modeling, .build() command workflow, query/scan access patterns, batch and transaction operations, and single-table design with computed keys. Use when implementing type-safe DynamoDB access layers with DynamoDB-Toolbox v2 in TypeScript services or serverless applications.
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Use when a user wants step-by-step help making an audio-first image-story, AI narration, slideshow, illustrated story, AI 讲书, 图片联播, 有声故事, or 静态图叙事视频 with Codex or WorkBuddy; not for a standalone script, single image, or ordinary video editing.
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Package a finished piece of work (spec, prototype, implementation notes) into a single document that gets reviewers to understanding and approval fast. Use when the user needs buy-in, a review, or a shareable summary of what was built and why.
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Turn real customer reviews, quotes, and case-study results into polished social-proof videos built in HyperFrames -- single-testimonial spotlights, review-wall montages, and stat-driven proof reels with captions and voiceover, cut for vertical, square, and wide. The highest-converting content most businesses never make.
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Combines GIFs and videos into composite tutorials with vertical or grid layouts via ffmpeg. Use when assembling multi-part media into a single output.
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Orchestrates multi-domain review (code, arch, tests, security) in a single pass. Use when thorough pre-release review is needed.
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。
Coordinates Claude agent teams via filesystem protocol. Use when orchestrating parallel agents with task dependencies. Do not use for single-agent tasks.
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。
Applies data-grid architecture for high-traffic stateful workloads. Use when a single database cannot scale and in-memory partitioning is needed.
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。