Results for “h5”

Exploratory data analysis (EDA) on a scientific data file — auto-detects the format, runs structure/quality/statistics checks, and writes a markdown EDA report with downstream recommendations. Use when asked to "explore", "analyze", "summarize", "profile", or "QC" a data file, or to understand its structure/content/quality before deciding what analysis to run. Covers tabular (.csv .tsv .xlsx .parquet), arrays (.npy .npz .hdf5 .h5 .mat .fits), sequence/genomics (.fasta .fastq .sam .bam .vcf .bed .gff .gtf .h5ad), microscopy (.tif .nd2 .czi .lif .ims .dcm .nii), spectroscopy/MS (.mzML .mzXML .mgf .fid .jdx), chemistry (.pdb .cif .mol .sdf .xyz .gro), and proteomics/metabolomics (.pepXML .mzid .mzTab). For zero-shot forecasting of a series use alterlab-timesfm; to create/configure a chunked cloud array store use alterlab-zarr. Part of the AlterLab Academic Skills suite.

Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations, concatenating batches, or handling layers/obsm/backed-mode; for the QC, normalization, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for RNA velocity from spliced/unspliced layers prefer alterlab-scvelo instead. Part of the AlterLab Academic Skills suite.

Build and operate a Havoc C2 framework for authorized red-team engagements, including team server deployment, evasive Demon agent generation, and post-exploitation.

Runs batch processing and high-performance computing (HPC) workloads on Google Kubernetes Engine (GKE), including job queues, parallel processing, and MPI workloads.

Selects the correct SageMaker serving container image URI for HuggingFace model deployments, prioritizing HuggingFace-curated Deep Learning Containers over generic alternatives.

Humanization Pipeline Orchestrator v3.1 - Multi-pass 4-layer transformation pipeline Orchestrates G5 (Auditor), G6 (Humanizer), F5 (Verifier) in sequential passes Enforces checkpoints between every pass with mandatory AskUserQuestion Supports conservative (L1-2), balanced (L1-3), balanced-fast (L1-3 merged), aggressive (L1-4) modes Rich Checkpoint v2.0: section-level scores, selective humanization, target auto-stop G5+F5 parallel execution, section-selective humanization Triggers: humanize, humanize my draft, humanize manuscript, make natural, remove AI patterns Korean triggers: 휴먼화, 자연스럽게, AI 패턴 제거

Deploy and configure the Havoc C2 framework with teamserver, HTTPS listeners, redirectors, and Demon agents for authorized red team operations.

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.

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.

Build, deploy, and interact with Juicebox V5 projects, including revnets, hooks, and omnichain deployments, with API references, implementation details, UI generation, and GraphQL queries.

Hedging Expert Advisor in Python with trailing stop and automated pending orders, converted from MQL5 and cross-platform compatible with mt5linux Docker.

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.

Meta's 7-8B specialized moderation model for LLM input/output filtering. 6 safety categories - violence/hate, sexual content, weapons, substances, self-harm, criminal planning. 94-95% accuracy. Deploy with vLLM, HuggingFace, Sagemaker. Integrates with NeMo Guardrails.

Run RNA velocity analysis with scVelo on single-cell RNA-seq data — estimate cell-state transitions from spliced/unspliced mRNA dynamics, infer trajectory direction, compute latent time, and identify driver genes. Use when adding directionality to trajectories or studying differentiation dynamics from spliced/unspliced layers (velocyto/STARsolo output); for the general QC, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for .h5ad data-structure I/O and layer wrangling prefer alterlab-anndata instead. Part of the AlterLab Academic Skills suite.

Run the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting. Use when analyzing scRNA-seq data through clustering, cell-type annotation, DE, or pseudotime workflows; for building or reading the .h5ad data structure itself (layers, obs/var, concatenation, backed mode) prefer alterlab-anndata instead, and for RNA velocity from spliced/unspliced counts prefer alterlab-scvelo instead. Part of the AlterLab Academic Skills suite.

Apply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretrained foundation model, generating scGPT embeddings, integrating batches with a transformer, or running zero-shot single-cell inference on an h5ad. For probabilistic latent models (scVI/scANVI) prefer alterlab-scvi-tools; for the standard QC→cluster→UMAP→DE pipeline prefer alterlab-scanpy; for the AnnData data structure itself prefer alterlab-anndata; for protein language models prefer alterlab-esm. Part of the AlterLab Academic Skills suite.