Results for “htslib”

Read, write, and analyze genomic datasets including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences using a Pythonic interface to htslib.

Use when you need to identify, view, or copy HTS-format files (BAM, CRAM, VCF, BCF). Use for inspecting file headers or viewing textual representations of binary HTS files.

Process whole slide images for digital pathology: detect tissue, extract tiles, and prepare datasets for deep learning pipelines.

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

Extract and preprocess tiles from whole-slide images (WSI) with histolab — OpenSlide-backed slide loading, tissue detection and masks, Random/Grid/Score tile extraction, and image/morphological filters for H&E preprocessing. Use when the user needs lightweight WSI slide preprocessing — building tile datasets for ML training, tissue segmentation, or quick tile-based inspection of histopathology slides. For end-to-end computational-pathology, deep-learning model training, nucleus segmentation, or multiplexed/spatial-proteomics (CODEX, Vectra) pipelines prefer alterlab-pathml instead. Part of the AlterLab Academic Skills suite.

Assess SSL/TLS server configurations using the sslyze Python library to evaluate cipher suites, certificate chains, protocol versions, HSTS headers, and known vulnerabilities like Heartbleed and ROBOT.

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.

Set up the Holoscan Sensor Bridge demo environment end-to-end: clone the repo, configure the host per platform, build and run the demo container, and verify connectivity to the sensor board.

Discover, select, and run Holoscan Sensor Bridge example applications on a connected devkit over SSH, filtering by platform, board type, and sensors.

Train or fine-tune language and vision models using TRL or Unsloth on Hugging Face Jobs cloud infrastructure, with support for SFT, DPO, GRPO, and reward modeling, plus GGUF conversion for local deployment.

Resolves, generates, and operates on media assets (audio, images, icons, logos, voice, color grades, LUTs) for HyperFrames projects, using a local cache and the HeyGen CLI for free-usage catalog search and TTS.

Simulates SSL stripping attacks using sslstrip, Bettercap, and mitmproxy in authorized environments to test HSTS enforcement, certificate validation, and HTTPS upgrade mechanisms.

TLS/SSL configuration audit. Tests protocol versions (SSLv2/3, TLS 1.0/1.1/1.2/1.3), cipher strength and ordering, certificate chain validation (intermediates, CT logs, OCSP stapling, pinning), known vulnerabilities (POODLE, BEAST, CRIME, Heartbleed, ROBOT, DROWN, Ticketbleed, GOLDENDOODLE), session management (ticket reuse, resumption, fixation), renegotiation attacks, TLS 1.3-specific issues (0-RTT replay, PSK modes, downgrade), HSTS deep analysis (preload, subdomains, bypass), and certificate revocation (CRL, OCSP responder, stapled response freshness). Compliance-mapped to PCI DSS 4.0 (full Section 4), NIST SP 800-52r2, and FedRAMP. Uses testssl.sh, sslscan, sslyze, openssl, nmap NSE scripts, and nuclei SSL templates. Multi-port scanning across 20+ TLS-bearing services.

Bundle TypeScript libraries with tsup — zero-config, powered by esbuild. Use when someone asks to "bundle a TypeScript library", "build npm package", "tsup", "publish TypeScript to npm", "build ESM and CJS", "bundle with esbuild", or "library bundling with zero config". Covers ESM/CJS dual output, declaration files, tree-shaking, and npm publishing.

Manages a local GitHub knowledge base and searches GitHub via the gh CLI, covering repos, issues, and pull requests.

Manage Hugging Face Hub resources via the `hf` CLI: download and upload models, datasets, and spaces; manage buckets, cache, collections, discussions, and inference endpoints; run SQL queries on datasets.

Bundle TypeScript and JavaScript libraries with blazing-fast speed powered by Rolldown. Use when building libraries, generating type declarations, bundling for multiple formats, or migrating from tsup.

Tracks multi-step work across sessions using the hzl CLI, coordinating sub-agents with checkpoints and leases.

Persistent task ledger for agent coordination. Plan multi-step work, checkpoint progress across session boundaries, and coordinate across multiple agents with project pool routing.

Discover and run Holoscan Sensor Bridge example applications on a connected devkit. Filters available apps by the user's platform, HSB software version, board type, and sensors. Supports timed execution, failure analysis, code-edit suggestions, and iterative re-runs.

Manage GitLab issues, merge requests, CI/CD pipelines, and repositories from the terminal using the glab CLI, including support for self-hosted instances and automation scripts.

Hugging Face Hub CLI (hf) — search, download, and upload models and datasets, manage repos, query datasets with SQL, deploy inference endpoints, manage Spaces and buckets.

Query the GTEx (Genotype-Tissue Expression) portal v2 REST API for tissue-specific gene expression (median TPM across 54 human tissues), expression QTLs (eQTLs), and splicing QTLs (sQTLs). Use when checking which tissues express a gene, finding which gene a non-coding/GWAS variant regulates via eQTLs, or interpreting variant regulatory effects across tissues. NOT for curated trait-variant associations (use alterlab-gwas), population allele frequencies or variant constraint (use alterlab-gnomad), or gene/transcript structure and ID mapping (use alterlab-ensembl). Part of the AlterLab Academic Skills suite.

Hugging Face Hub CLI (hf) — search, download, and upload models and datasets, manage repos, query datasets with SQL, deploy inference endpoints, manage Spaces and buckets.

Bundle TypeScript and JavaScript libraries with blazing-fast speed powered by Rolldown. Use when building libraries, generating type declarations, bundling for multiple formats, or migrating from tsup.

Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export PNG/PDF/SVG, for scientific visualization and publication figures.

Build, edit, and deploy full-stack websites or web apps using the Higgsfield CLI, with two distinct product types: standalone websites or Higgsfield-integrated apps.

Leads the five daily Islamic prayers and Friday khutbahs via text-to-speech, with multilingual support and step-by-step vocal guidance.

Operate Hugging Face Hub repositories, models, datasets, and Spaces via the hf CLI, including downloads, uploads, authentication, and compute jobs.

Configure Hardware Security Modules (HSMs) using the PKCS#11 standard interface for key generation, signing, encryption, and key management with both physical HSMs and SoftHSM2 for development.

Converts text to speech and generates MP3 audio files using Hume AI or OpenAI APIs, printing the file path for delivery.

Manage production secret infrastructure with HashiCorp Vault, cloud secret stores, automated rotation, and audit logging.

Tracks multi-step work across sessions using the hzl CLI, coordinating sub-agents with projects, tasks, checkpoints, and leases.

Create publication-quality static, animated, and interactive plots with fine-grained control over every element, from basic charts to multi-panel figures, with export to PNG, PDF, and SVG.