'bulk' 검색 결과

JIRA search + filter management via jira-as; JQL injection-safe. NOT single-issue CRUD (mk:jira-issue) or bulk writes (mk:jira-bulk).

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Confluence comments, attachments, labels, watchers via confluence-as. Inline-vs-footer safety enforced. NOT page CRUD (mk:confluence-page) or bulk ops (mk:confluence-bulk).

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Confluence page CRUD via confluence-as: create/show/update/delete, hierarchy, copy. NOT bulk (mk:confluence-bulk), spec analysis (mk:confluence-spec-analyst), or comments (mk:confluence-collaborate).

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Confluence CQL search, space list, saved filters, export via confluence-as; CQL injection-safe. NOT single-page CRUD (mk:confluence-page) or bulk writes (mk:confluence-bulk).

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JIRA issue CRUD via the jira-as wrapper. Triggers: 'create bug/task/story', 'show me PROJ-123', 'get/view/look up issue', 'update PROJ-123', 'delete PROJ-123'. NOT for transitions (mk:jira-lifecycle); NOT for comments/attachments (mk:jira-collaborate); NOT for bulk ops (mk:jira-bulk); NOT for issue links (mk:jira-relationships); NOT for time logging (mk:jira-time); NOT for sprint/epic (mk:jira-agile).

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Drive JIRA workflow lifecycle via the jira-as wrapper: transition, assign, resolve, reopen, manage versions and components. Triggers: 'transition KEY to Status', 'mark KEY as Done', 'assign KEY to user', 'reopen KEY', 'release version', 'create component'. NOT for issue CRUD (mk:jira-issue); NOT for bulk transitions (mk:jira-bulk).

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JIRA search + filter management via the jira-as wrapper. Triggers: 'search jira', 'find issues where X', 'jql for ...', 'export search results', 'manage saved filters'. JQL injection-safe via the shared sanitizer. NOT for single-issue CRUD (mk:jira-issue); NOT for bulk write ops (mk:jira-bulk).

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JIRA time tracking via the jira-as wrapper: log work, list/update/delete worklogs, set estimates, generate reports, bulk-log. Triggers: 'log 2h on KEY', 'show worklog for KEY', 'time report for sprint', 'bulk-log 30m to JQL'. Worklog edit/delete loses data — agent confirms. NOT for sprint capacity (mk:jira-agile).

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Manage Confluence collaboration surface via the confluence-as wrapper: comments, attachments, labels, watchers. Triggers: 'add comment to page 12345', 'upload attachment to page 12345', 'label page 12345 as urgent', 'watch page 12345'. Inline-vs-footer comment safety enforced. NOT for page CRUD (mk:confluence-page); NOT for bulk ops (mk:confluence-bulk).

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Confluence CQL search + space list + saved-filter + export via the confluence-as wrapper. Triggers: 'search confluence', 'find pages where X', 'cql for ...', 'export search results', 'list spaces', 'manage saved filters'. CQL injection-safe via the shared sanitizer. NOT for single-page CRUD (mk:confluence-page); NOT for bulk write ops (mk:confluence-bulk).

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Confluence page CRUD via the confluence-as wrapper. Triggers: 'create page in SPACE', 'show me page 12345', 'update title of page 12345', 'delete page 12345', 'page hierarchy under 12345', 'copy page 12345 to SPACE'. NOT for bulk ops on 10+ pages (mk:confluence-bulk); NOT for spec analysis (mk:confluence-spec-analyst); NOT for comments/attachments/labels (mk:confluence-collaborate).

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Passive domain reconnaissance using Python stdlib. Use this skill for subdomain discovery, SSL certificate inspection, WHOIS lookups, DNS records, domain availability checks, and bulk multi-domain analysis. No API keys required. Triggers on requests like "find subdomains", "check ssl cert", "whois lookup", "is this domain available", "bulk check these domains".

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Crawl websites and extract content from multiple pages via the Tavily CLI. Use this skill when the user wants to crawl a site, download documentation, extract an entire docs section, bulk-extract pages, save a site as local markdown files, or says "crawl", "get all the pages", "download the docs", "extract everything under /docs", "bulk extract", or needs content from many pages on the same domain. Supports depth/breadth control, path filtering, semantic instructions, and saving each page as a local markdown file.

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Orchestrates an end-to-end immune-repertoire pipeline from FASTQ to clonotypes, diversity, overlap, somatic hypermutation and lineages, routing on two forks. Use when deciding bulk vs single-cell (bulk amplicon/RNA-seq -> MiXCR analyze preset -> VDJtools/immunarch depth-normalized diversity and overlap -> figures; 10x paired VDJ -> MiXCR 10x preset or Cell Ranger -> scirpy gene-expression integration, chain QC, clonotype clusters); and TCR vs BCR (TCR -> exact CDR3-nt+V/J clonotypes, VDJtools diversity is fine; BCR -> somatic hypermutation makes exact clonotypes wrong -> Immcantation distToNearest/findThreshold clonal clustering, germline reconstruction, SHM, Dowser lineages); selecting the MiXCR 4.x preset by chemistry and activating its license; downsampling to equal depth before comparing diversity or overlap; and optionally annotating antigen specificity.

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End-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq. Aligns with STAR 2-pass cohort-style, performs junction QC (RSeQC, MaxEntScan, SpliceAI), runs rMATS-turbo and leafcutter for concordant differential analysis, optionally MAJIQ V3 for complex events / heterogeneous cohorts, isoform-switching with NMD/ORF/domain consequences (IsoformSwitchAnalyzeR v2 + DRIMSeq+DEXSeq+stageR DTU), and sashimi visualizations. Use when performing comprehensive splicing analysis from raw bulk RNA-seq data; for variant-driven splice prediction see splice-variant-prediction; for rare-disease single-patient outlier detection see outlier-splicing-detection; for full-isoform PacBio/ONT analysis see long-read-splicing.

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SQLAlchemy 2.x patterns for async FastAPI projects: models, sessions, queries, bulk operations, transactions, and Alembic migrations. Trigger: When writing models, queries, bulk operations, or DB-touching service code.

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Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity from regulons with VIPER and msVIPER. Covers the activity-not-edges paradigm, the undirected-association caveat, the DREAM5 wisdom-of-crowds and method-complementarity result, AUPRC-over-AUROC evaluation, and gold-standard incompleteness. Use when inferring a regulatory network from a bulk expression matrix, finding master regulators, or scoring TF activity from a signature. For single-cell motif-pruned regulons see scenic-regulons; for co-expression modules see coexpression-networks.

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Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR (Python) implicit transpose, AnnData (cells-rows) <-> SingleCellExperiment (cells-cols) orientation flip, HDF5/h5ad vs Zarr cloud-native shift, HDF5SummarizedExperiment + DelayedArray for out-of-memory bulk, scanpy backed mode for large h5ad, the ~10-15% density crossover where dense beats sparse, 10X format proliferation (MTX vs CellRanger H5 vs h5ad), the dense-conversion memory blow-up, and Dask + Zarr for consortium-scale matrices. Use when choosing sparse format, working with single-cell-sized matrices, importing/exporting 10X, debugging R/Python interop transposes, processing matrices too large for RAM, or building cloud-native pipelines.

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Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against testing on a batch-corrected matrix, the choice between SVA/RUVg/RUVs/RUVr, the confounding non-identifiability problem, the single-cell boundary (Harmony/MNN are NOT for bulk), and the Goh 2017 harmonization critique. Use when designing a DE analysis with batch structure, troubleshooting batch-dominated PCA, choosing ComBat vs ComBat-seq, handling unknown batch via SVA, integrating across studies, or deciding when (rarely) to subtract batch.

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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing, apeglm/ashr/normal LFC shrinkage, independent filtering, Cook's outlier handling, VST/rlog transforms, and design formulas including paired, batch, and interaction terms. Use when running bulk DE, choosing DESeq2 over edgeR or limma-voom, building a paired or interaction design, applying LFC shrinkage for ranking or GSEA, choosing Wald vs LRT, troubleshooting padj=NA, picking VST vs rlog, importing salmon/kallisto via tximport, or analyzing prokaryotic RNA-seq.

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Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.

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Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).

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Audit and update metadata across multiple AEM Edge Delivery Services pages. Scans pages via the query index, identifies missing or inconsistent metadata (titles, descriptions, og tags, robots), and generates a corrected bulk metadata spreadsheet. Use when standardizing metadata across a site, preparing for launch, or fixing SEO issues at scale.

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