Results for “pe-files”

Calculates polygenic risk scores from 23andMe or AncestryDNA genotype files using PGS Catalog scoring files, then estimates population percentiles and risk categories.

Trains machine learning models on genomic interval data from BED files, including region embeddings, single-cell ATAC-seq analysis, and consensus peak building.

Extracts and analyzes firmware images using binwalk to identify embedded filesystems, compressed archives, bootloaders, kernel images, and cryptographic material. Covers entropy analysis, recursive extraction, filesystem mounting, and string analysis for credential and configuration discovery.

Manipulate biological sequences, parse FASTA/GenBank/PDB files, access NCBI databases, run BLAST searches, and perform phylogenetics using the Biopython library.

Detect and extract hidden data embedded in images, audio, and other media files using steganalysis tools to uncover covert communication channels.

Recover deleted records, analyze freelist pages, WAL files, and unallocated space in SQLite databases for digital forensics and incident response.

Use DuckDB from MATLAB via Database Toolbox (R2026a+) as a non-math operations engine on large tabular files (CSV/Parquet/JSON) and as a zero-config embedded database. Use when connecting to DuckDB, querying CSV, Parquet, and JSON files directly with SQL, reducing or profiling large data before MATLAB analysis, creating portable development databases, or installing DuckDB extensions. Triggers on: DuckDB, duckdb(), large CSV/Parquet/JSON, file too large for readtable, filter/aggregate at source, deduplicate, reduce before analysis, profile large file, persistent file import, analytical engine, SQL on CSV, SQL on Parquet, SQL on JSON, query CSV with SQL, query Parquet with SQL, run SQL on files, SQL queries on files, query files directly, SQL without database, in-process SQL.

Analyze network packet captures (PCAP/PCAPNG) using Wireshark, tshark, tcpdump, and Python to reconstruct communications, extract files, and identify malicious traffic.

Perform comprehensive forensic analysis of disk images using Autopsy to recover files, examine artifacts, and build investigation timelines.

Manage AWS S3 buckets and objects: create buckets, upload/download files, configure lifecycle policies, set up static websites, manage permissions, and implement cross-region replication.

Analyze git repositories to build a security ownership topology mapping people to files, compute bus factor and sensitive-code ownership, and export CSV/JSON for graph databases and visualization.

Construye pipelines ETL/ELT con Pandas: extracción, transformación y carga de datos con logging, manejo de errores, idempotencia y opciones de orquestación.

Apache Airflow, dbt, Prefect, Dagster, and modern data orchestration for production data pipelines

Personal protective equipment tracker. Use when json ppe tasks, csv ppe tasks, checking ppe status.

Write, review, debug, test, and optimize Python Polars code with version-grounded object types, schemas, and execution boundaries.

Run SQL queries and psql meta-commands against PostgreSQL databases via the psql CLI, with options for file execution, tuples-only output, and timeouts.

Analyzes malware-generated network traffic from PCAP files to identify C2 protocols, data exfiltration, DNS tunneling, and beaconing patterns using Wireshark, Zeek, Suricata, and Python.

Automates packet capture analysis using tshark and pyshark to extract protocol statistics, detect suspicious flows, identify IOCs, and analyze DNS anomalies from PCAP files.

Build ETL pipelines with data ingestion, cleaning, and validation steps. Use when ingesting sources, transforming formats, validating data, or scheduling loads.

Analyze proteomics and metabolomics mass spectrometry data with PyOpenMS: read/write MS file formats, process spectra, detect and quantify features, identify peptides and proteins, and run end-to-end LC-MS/MS pipelines using ready-to-run scripts.

Guides analysis of Neuropixels recordings from raw data to curated units, covering preprocessing, motion correction, spike sorting, quality metrics, and export.

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.

Use this skill when the user uploads Excel (.xlsx/.xls) or CSV files and wants to perform data analysis, generate statistics, create summaries, pivot tables, SQL queries, or any form of structured data exploration. Supports multi-sheet Excel workbooks, aggregation, filtering, joins, and exporting results to CSV/JSON/Markdown.

Access NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download microarray and RNA-seq datasets by GSE, GSM, GPL, or GDS accession and retrieve SOFT, MINiML, and series matrix files. Use when locating public expression datasets, fetching processed expression matrices, downloading a study's supplementary files, or sourcing per-study transcriptomics data for differential-expression analysis. For raw FASTQ sequencing reads by SRA/ENA run accession use alterlab-ena; for reference tissue-expression baselines (median TPM across human tissues) use alterlab-gtex; for cancer cohort somatic mutations and copy-number use alterlab-cbioportal. Part of the AlterLab Academic Skills suite.

After a Content Factory run completes successfully, harvest prompts, character references, cost data, and quality scores; diff them against the canonical prompt_registry and character_identity store; open improvement PRs (prompt updates + new character references). Runs ONCE per successful run, then closes. Also files findings into a CF_IMPROVER_ISSUES.csv (Intelliverse audit framework pattern) for the librarian's weekly roll-up.

Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that do not fit in memory.

Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that don't fit in memory.

Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that don't fit in memory.

Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that don't fit in memory.