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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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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.

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Process many sequence files in batch (count, merge, split, convert, summarize) with memory-safe streaming and on-disk indexing using Biopython, pysam, or pyfastx. Use when iterating over a directory of FASTA/FASTQ files, merging or splitting datasets, building random access across many or huge files, or automating per-file operations without exhausting RAM.

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Process and generate multimedia content using Google Gemini API. Capabilities include analyze audio files (transcription with timestamps, summarization, speech understanding, music/sound analysis up to 9.5 hours), understand images (captioning, object detection, OCR, visual Q&A, segmentation), process videos (scene detection, Q&A, temporal analysis, YouTube URLs, up to 6 hours), extract from documents (PDF tables, forms, charts, diagrams, multi-page), generate images (text-to-image, editing, composition, refinement). Use when working with audio/video files, analyzing images or screenshots, processing PDF documents, extracting structured data from media, creating images from text prompts, or implementing multimodal AI features. Supports multiple models (Gemini 2.5/2.0) with context windows up to 2M tokens.

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Apache Spark 4.0.2 best practices for PySpark and Scala distributed data processing

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Use when choosing .NET concurrency patterns for async I/O, queues, pipelines, or thread safety. Keywords: async/await, channels, dataflow, Rx, lock contention, producer consumer, parallel processing.

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Use this skill when a data processing agreement is being negotiated or renewed and someone asks "review the TOMs annex", "check the security measures in this DPA", "can we sign this annex", "the customer sent their DPA with a security schedule", "is our standard annex still true" or "does this vendor's annex promise enough". Breaks the technical and organisational measures annex into single commitments, compares each one with what the company actually runs or with what the use case needs, and writes a line-by-line review, proposed redlines and a list of practice gaps for owners.

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Process and manipulate images using ImageMagick. Supports resizing, format conversion, batch processing, and retrieving image metadata. Use when working with images, creating thumbnails, resizing wallpapers, or performing batch image operations.

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Extract text, tables, and structured data from documents using Azure Document Intelligence (@azure-rest/ai-document-intelligence). Use when processing invoices, receipts, IDs, forms, or building custom document models.

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Azure AI Document Intelligence SDK for .NET. Extract text, tables, and structured data from documents using prebuilt and custom models. Use for invoice processing, receipt extraction, ID document analysis, and custom document models. Triggers: "Document Intelligence", "DocumentIntelligenceClient"...

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Leverages Splunk Enterprise Security and SPL (Search Processing Language) to investigate security incidents through log correlation, timeline reconstruction, and anomaly detection. Covers Windows event logs, firewall logs, proxy logs, and authentication data analysis. Activates for requests involving Splunk investigation, SPL queries, SIEM log analysis, security event correlation, or log-based incident investigation.

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Extract structured data from receipts and invoices for bookkeeping, expense tracking, and tax preparation. Supports email, photos, scanned images, PDFs, and accounting exports. Outputs vendor, date, amount, tax, line items as table, CSV, or JSON. Trigger on "process receipts", "extract receipts from email", "scan invoices", "capture expenses".

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Draft privacy policies, terms of service, disclaimers, and legal notices. Creates GDPR-compliant texts, cookie policies, and data processing agreements.

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Implement PCI DSS compliance requirements for secure handling of payment card data and payment systems. Use when securing payment processing, achieving PCI compliance, or implementing payment card security measures.

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Extract text, tables, and structured data from documents using Azure Document Intelligence (@azure-rest/ai-document-intelligence). Use when processing invoices, receipts, IDs, forms, or building cu...

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Develop, debug, and deploy Apify Actors - serverless cloud programs for web scraping, automation, and data processing. Use when creating new Actors, modifying existing ones, or troubleshooting Acto...

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Expert en eDiscovery (document review, data processing, ESI, litigation hold, TAR)

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Collect, download, and verify App Store Connect Analytics reports with asc. Use when users need to discover analytics report requests, select report instances by processing date or granularity, download every segment, or verify downloaded files against Apple's size and MD5 metadata before analysis.

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Implements AWS Nitro Enclave-based confidential computing environments with cryptographic attestation, KMS policy integration using PCR-based condition keys, and secure vsock communication channels. The practitioner builds enclave images, configures attestation-aware KMS policies, validates attestation documents against the AWS Nitro PKI root of trust, and establishes isolated computation pipelines for processing sensitive data such as PII, cryptographic keys, and healthcare records. Activate...

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Leverages Splunk Enterprise Security and SPL (Search Processing Language) to investigate security incidents through log correlation, timeline reconstruction, and anomaly detection. Covers Windows event logs, firewall logs, proxy logs, and authentication data analysis. Activates for requests involving Splunk investigation, SPL queries, SIEM log analysis, security event correlation, or log-based incident investigation.

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Frequency-domain analysis — FFT, power spectral density (Welch/periodogram), spectrograms, wavelet transforms, and coherence. Use for any signal with periodic, quasi-periodic, or transient frequency content in physics data.

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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.

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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.

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End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with limma (default) or MSstats for complex feature-level designs. Use when processing mass spectrometry proteomics.

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