Tag: rna-seq

Type: All Skills Tools
Tags: mcp automation llm cli code-review unity typescript genomics game-development bioinformatics debugging documentation cloudbase ai-agents agentic-workflow devops llm-agent workflow-automation encode code-analysis
skill ★ 34

ENCODE Multi-Omics Data Integration

Integrates multiple ENCODE data types, including RNA-seq, ATAC-seq, and ChIP-seq, to construct a comprehensive regulatory landscape for specific tissues or cell types. It enables chromatin state annotation, enhancer-gene linkage, and the ch…

ammawla/encode-toolkit multi-omics encode epigenomics bioinformatics
tool ★ 34

ENCODE RNA-seq Quantification Pipeline

This tool executes a comprehensive, ENCODE-standard RNA-seq pipeline using Nextflow. It processes raw FASTQ data through STAR alignment, generating gene/transcript quantification (TPM/FPKM) and strand-specific bigWig signal tracks.

ammawla/encode-toolkit rna-seq gene-expression quantification star-alignment
skill ★ 34

Setup reproducible bioinformatics environments for ENCODE

This skill provisions fully reproducible, version-pinned computational environments for diverse ENCODE assays, generating conda definitions, R/Bioconductor scripts, and Python requirements. It simplifies the setup of complex pipelines (e.g.…

ammawla/encode-toolkit bioinformatics conda-environment reproducibility enode-data