1.7万 件 ・ 関連度順
概要と使いどころ
Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. Use for batch processing, custom pipelines, format conversion, PubMed/GenBank queries. For quick gene lookups use gget; for multi-service REST APIs use bioservices.
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Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic trees (Phylo). Use for gene family studies, phylogenomics, comparative genomics, NCBI pipelines. For PCR/restriction/cloning use biopython-molecular-biology; for SAM/BAM use pysam.
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Point Cowork at a folder of medical bills and insurance EOBs -- matches every bill to its explanation of benefits, catches duplicate charges, balance-billing, and bills that ignore your insurance, then drafts the dispute letters and phone scripts. Most medical bills contain errors; this finds them.
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Addresses HIPAA privacy and security requirements for health data interoperability under the 21st Century Cures Act, ONC Health IT Certification Program, and CMS Interoperability and Patient Access Final Rule. Covers information blocking prohibitions, FHIR API patient access, TEFCA exchange purposes, and privacy safeguards for health information exchange. Keywords: interoperability, information blocking, FHIR, TEFCA, Cures Act, patient access API, health information exchange.
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Interact with Hacker News (news.ycombinator.com) — browse top, new, and best stories, read item details and comment threads, look up user profiles, and search posts via Algolia. Use this skill whenever the user mentions Hacker News, HN, YCombinator news, ycombinator.com, news.ycombinator.com, wants to browse tech news, read HN discussions, search HN posts, or look up HN users. Also trigger when the user pastes an HN URL (e.g. news.ycombinator.com/item?id=12345). Keywords: Hacker News, HN, YC, ycombinator, tech news, Show HN, Ask HN, HN front page.
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Apply the bioengineering, translational systems biology, and tissue modeling frameworks of Linda Griffith, Professor of Biological Engineering at MIT and tissue engineering pioneer. Use this skill whenever facing decisions, designs, or evaluations in bioengineering, tissue modeling, microphysiological systems (organs-on-chips), synthetic matrix design, disease subtyping, or drug target validation. Reach for this skill when evaluating preclinical models (human vs. animal), reframing overlooked or neglected pathologies into rigorous engineering challenges, selecting biomaterials, designing cell signal processing assays, or diagnosing operational flaws in experimental platforms (e.g., PDMS compound absorption or Matrigel lot variability).
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Audit web pages for accessibility issues, WCAG compliance, and screen reader compatibility. Trigger when the user asks to: check accessibility, run an a11y audit, test WCAG compliance, check screen reader support, audit ARIA attributes, verify keyboard navigation, find accessibility issues, or check for missing alt text or labels.
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Analyze CVE reachability in software repositories by examining how vulnerable dependencies are imported and used. Determines whether vulnerable components, classes, or functions are reachable from project code through call chain analysis, reflection detection, dynamic loading patterns, and configuration-gated behavior. Classifies each CVE as likely reachable, possibly reachable, or likely unreachable with supporting evidence. Use when analyzing security vulnerabilities in dependencies, performing post-disclosure CVE triage, assessing vulnerability impact, or when users ask to analyze CVE reachability, check if vulnerabilities are exploitable, or evaluate dependency security risks.
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Think and work like an expert Marine Biologist. Use when a task calls for Marine Biologist judgment. Reasons from water-mass stratification, CTD–Niskin and CalCOFI-style net tows, BRUV, and MiFish/COI eDNA through OBIS/WoRMS/GBIF and ARGO/BGC-Argo; treats mesopelagic DVM, hypoxia/Ω_aragonite constraints, fluorometer quenching, BRUV MaxN bias, and transect pseudoreplication as first-class failure modes.
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Think and work like an expert Herpetologist. Use when a task calls for Herpetologist judgment. Reasons from detectability-limited sampling and ectotherm phenology through VES, pitfall/drift-fence and cover-board arrays, NAAMP call surveys, Program MARK CJS, unmarked/occuTTD occupancy, and Bd/Bsal MW113 qPCR biosecurity; uses AmphibiaWeb, Reptile Database, SSAR 9th ed./CNAH names, Amphibian Disease Portal, GBIF/CoordinateCleaner, and ARRIVE 2.0 while treating weather bias, pitfall selectivity, and pathogen cross-contamination as first-class failure modes.
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Think and work like an expert Combinatorialist. Use when a task calls for Combinatorialist judgment. Reasons from labelled vs unlabelled enumeration, EGF/OGF and species, bijective and probabilistic proofs, Turán/Ramsey/extremal bounds, and BIBD/OA design parameters through SageMath/GAP/nauty, OEIS, House of Graphs, and Colbourn–Dinitz tables while treating isomorphism double-counting, parity barriers, and OEIS false matches as first-class failure modes.
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Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by keyword, building reproducible field-qualified queries, navigating the Entrez Query Translator, exploiting the history server for large result sets, handling retmax caps, or interpreting weekly index lag. Covers PubMed, Nucleotide, Protein, Gene, SRA, GEO, Assembly, Taxonomy, ClinVar, dbSNP.
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Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.
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Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.
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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.
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Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identifying taxa that differ between experimental groups while accounting for the compositional nature of microbiome data.
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Per-CpG differential methylation testing from bisulfite sequencing count data or beta-value matrices. Covers beta and M-value computation, coverage filtering, statistical tests (Welch t-test, Mann-Whitney, limma, DSS beta-binomial), multiple testing correction, and effect size calculation. Use when comparing methylation at individual CpG sites between experimental groups from WGBS, RRBS, or targeted bisulfite sequencing.
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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.
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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.
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。
Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample dissimilarity with phyloseq and vegan. Use when comparing community composition across samples or testing for group differences in microbiome structure.
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Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or EnFormer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.
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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.
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。
Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.
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 ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIAS footprinting. Use when running end-to-end ATAC-seq analysis from FASTQ to differential accessibility.
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。