Skill UI

Generates ORM models and database schemas for frameworks like TypeORM, Prisma, Sequelize, SQLAlchemy, Django ORM, Entity Framework, and Hibernate, translating user requests into ready-to-use model code or schema definitions to accelerate backend development.

Arboreto infers gene regulatory networks from bulk or single-cell RNA-seq data using scalable GRNBoost2 and GENIE3 algorithms, letting researchers filter transcription-factor targets, run distributed Dask jobs, and export ranked links for downstream analysis.

deepTools is a Python command-line suite for NGS workflows, converting BAM files into normalized coverage, running QC (fingerprint, correlation, PCA), comparing samples, and rendering heatmaps or profiles for ChIP-seq, RNA-seq, and ATAC-seq analyses.

Access the European Nucleotide Archive via REST/FTP to fetch DNA/RNA sequences, raw reads, assemblies, annotations, and taxonomy for research or bioinformatics pipelines.

LatchBio Integration provides a Python-first platform to compose, deploy, and monitor serverless bioinformatics pipelines with the Latch SDK, decorator-based tasks, cloud storage (LatchFile/Dir), GPU tuning, and Nextflow or Snakemake interoperability.

PyDESeq2 brings the DESeq2 differential expression workflow to Python, letting users load bulk RNA-seq counts, specify design formulas, fit DESeq2 models, run Wald tests with FDR correction, optionally apply apeGLM shrinkage, and export gene-level statistics within pandas/AnnData pipelines.

Scanpy is a scalable Python toolkit for single-cell RNA-seq analyses, covering QC, normalization, dimensionality reduction, clustering, marker discovery, annotation, and publication-ready visualization across h5ad/10X/CSV datasets.

Provide a comprehensive toolkit for RNA velocity inference in single-cell RNA-seq data, modeling unspliced/spliced kinetics to infer differentiation directions, latent time, and driver genes while complementing Scanpy pipelines.

RecallMax dramatically enhances AI agent memory capabilities by cleanly injecting massive external contexts (500K-1M tokens) without hallucination drift. It automatically summarizes lengthy conversations, preserving tone, intent, and key facts. Furthermore, it compresses multi-turn interaction histories into high-density token sequences, ensuring agents maintain perfect recall across complex and long-running sessions.

This skill helps developers structure and record critical architectural decisions (ADRs) made during coding sessions. It automatically detects moments of decision, capturing the context, alternatives considered, and the rationale (trade-offs and consequences). This maintains a living log that explains 'why' the code base was built the way it is, preventing knowledge loss and improving project maintainability.

AnnData is a specialized Python package designed for managing and analyzing annotated matrices, particularly crucial in single-cell genomics and bioinformatics. It efficiently stores experimental measurements (X) alongside comprehensive metadata (obs, var, obsm, etc.). This skill allows users to read, write, subset, and concatenate large, complex datasets in formats like .h5ad and .zarr, making it essential for scRNA-seq analysis workflows and integration with the scverse ecosystem.

Arboreto is a powerful Python library designed to infer Gene Regulatory Networks (GRNs) from various gene expression datasets, including bulk and single-cell RNA-seq. It employs scalable algorithms like GRNBoost2 and GENIE3 to identify critical transcription factor-target gene relationships. Featuring support for Dask distributed computing, Arboreto is optimized for large-scale, high-throughput transcriptomic analysis.