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bio-metagenomics-functional-profiling
【数据与研究】Profiles the functional potential of shotgun metagenomes with HUMAnN 3's tiered search (MetaPhlAn prescreen, Bowtie2 pangenome, translated DIAMOND vs UniRef), giving gene-family (RPK) and MetaCyc pathway abundances stratified by species. Covers why a metagenome measures potential not activity, why dropping UNMAPPED/UNINTEGRATED biases everything, why…
bio-rna-quantification-tximport-workflow
【数据与研究】Import transcript-level quantifications from Salmon/kallisto/RSEM into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when summarizing transcript abundances to gene counts with the correct length offset, choosing a countsFromAbundance mode (full-length vs 3'-tag vs DTU), resolving transcript-ID version mismatches, or handi…
bio-workflows-metagenomics-pipeline
【效率与协作】End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host depletion, Kraken2+Bracken classification, MetaPhlAn marker profiling, and HUMAnN functional profiling. Covers the controls-first ordering, why Kraken2 read counts are not abundances and MetaPhlAn cell fractions do not equal Bracken r…
sanity-singletons
【文档与办公】Configure singleton documents in a Sanity Studio using the document.singletons registry. Use when a developer wants a fixed-id document (settings, navigation, footer) edited in place, hidden from the default content list, with no "create new" or "duplicate" affordances — or when migrating a userland singleton implementation or a third-party singleton…
critique-affordance
【效率与协作】Critique a screen's interactive affordances — what looks clickable, state visibility, CTA clarity, and action discoverability.
securite-anssi
【开发与工程】Règles essentielles de sécurité ANSSI pour le développement d'applications de l'État. 12 règles couvrant TLS, secrets, authentification, headers, dépendances, entrées, logs et durcissement. Utiliser cette skill quand l'utilisateur développe une application web, une API, ou tout service exposé, quand il mentionne la sécurité, l'ANSSI, le durcissement,…
security-dependency-audit
【效率与协作】Audit de sécurité des dépendances — détection de vulnérabilités connues, mises à jour critiques et gestion du cycle de vie des packages. À utiliser quand l'utilisateur veut vérifier la sécurité de ses dépendances, mettre à jour des packages vulnérables ou mettre en place un processus d'audit continu. Se déclenche aussi avec "audit dépendances", "vuln…
semiotics
【设计与创意】Use when designing or auditing icon systems, colors/badges/shapes, visual metaphors, interface signs, or naming-plus-visual surfaces that users misread. Covers semiotic reasoning across icon/index/symbol, signifier/signified, denotation/connotation/myth, color/shape/position/iconography, affordances, code/API signifiers, and semiotic-coherence audits…
affordances
【效率与协作】Los objetos deben sugerir cómo se usan. Use cuando diseñe botones, controles interactivos, o cualquier elemento que invite a la acción.
affordances
【效率与协作】Los objetos deben sugerir cómo se usan. Use cuando diseñe botones, controles interactivos, o cualquier elemento que invite a la acción.
affordances
【效率与协作】Los objetos deben sugerir cómo se usan. Use cuando diseñe botones, controles interactivos, o cualquier elemento que invite a la acción.
bio-metagenomics-abundance
【效率与协作】Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed from Kraken2 classification output.
bio-metagenomics-abundance
【效率与协作】Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed from Kraken2 classification output.
bio-metagenomics-abundance
【效率与协作】Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed from Kraken2 classification output.
bio-metagenomics-functional-profiling
【数据与研究】Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.
bio-metagenomics-metaphlan
【效率与协作】Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers. Use when accurate taxonomic profiling is needed and computational resources are limited, or for comparison with HMP/other MetaPhlAn studies.
bio-microbiome-functional-prediction
【数据与研究】Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables. Use when functional profiling is needed from 16S data without shotgun metagenomics sequencing.
bio-proteomics-quantification
【数据与研究】Protein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT, iTRAQ), and metabolic labeling (SILAC) approaches. Use when extracting protein abundances from MS data for differential analysis.