Results for “h5ad”
11 skills
smith6jt-cop h5ad-shiny-data-pipeline
Patterns for H5AD-backed Shiny apps with Excel fallback, groovy data in .uns, scVI QC validation, Leiden clustering merge, per-donor tissue extraction
3
alterlab-ieu alterlab-anndata
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.
60 · bundle
alterlab-ieu alterlab-scvelo
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.
60 · bundle
More results
alterlab-ieu alterlab-scanpy
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.
60 · bundle
nvidia cupynumeric-hdf5
Read and write large cuPyNumeric arrays to HDF5 files using Legate's parallel, distributed HDF5 I/O.
2.2k · bundle
nimoqup046-collab loki-mode
Runs an autonomous multi-agent software development pipeline that takes a PRD through to production with zero human intervention, using model-tiered agents, memory, and verification cycles.
2 · bundle
mukul975 operating-havoc-c2
Build and operate a Havoc C2 framework for authorized red-team engagements, including team server deployment, evasive Demon agent generation, and post-exploitation.
24.6k · bundle
pwdev-solucoes kubernetes-platform
Diagnoses and operates Kubernetes clusters: pods, deployments, ingress, HPA, PVC, StorageClass, NetworkPolicy, Secrets, Helm, ArgoCD, cert-manager. Reads before changing; mutations require confirmation and diff review.
2
aibot88 keda
Configure, operate, and master KEDA (Kubernetes Event-driven Autoscaling) — ScaledObject, ScaledJob, TriggerAuthentication CRDs, 70+ scalers, HPA behavior tuning, scale-to-zero, the KEDA HTTP Add-on, production hardening, multi-trigger semantics, scalingModifiers formulas, GitOps integration, and troubleshooting stuck scalers. Covers the common traps (cooldownPeriod only applies to N→0, CPU/memory cannot drive scale-to-zero alone, activationThreshold vs threshold, multi-trigger max-of semantics, HPA conflicts).
3 · bundle
alterlab-ieu alterlab-scgpt
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.
60 · bundle
alterlab-ieu alterlab-eda
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.
60 · bundle