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Search RNA-Seq , found 12 results

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Arboreto GRN Inference

K-Dense-AI/claude-scientific-skills

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.

NGS Data Visualization

K-Dense-AI/claude-scientific-skills

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.

ENA Sequence Access

K-Dense-AI/claude-scientific-skills

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

PyDESeq2 Differential Analysis

K-Dense-AI/claude-scientific-skills

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 Single-Cell Workflow

K-Dense-AI/claude-scientific-skills

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.

scVelo RNA Velocity Workflow

K-Dense-AI/claude-scientific-skills

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.

Arboreto GRN Inference

K-Dense-AI/scientific-agent-skills

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.

NGS Data Visualization

K-Dense-AI/scientific-agent-skills

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.

PyDESeq2 Differential Analysis

K-Dense-AI/scientific-agent-skills

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 Single-Cell Workflow

K-Dense-AI/scientific-agent-skills

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.

scVelo RNA Velocity Workflow

K-Dense-AI/scientific-agent-skills

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.

Orchestrating Hex Projects via API

hex-core-workflow-a

jeremylongshore/claude-code-plugins-plus-skills

This skill provides the core mechanism for integrating Hex into external data pipelines. It enables triggering, monitoring, and managing Hex projects (e.g., via Airflow or Dagster) programmatically. Users can implement parameterized runs, execute multi-step ETL workflows sequentially, and handle status polling and error management, making it ideal for production data orchestration.

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