Can I perform data normalization with this skill?

Yes, it supports multiple normalization methods such as RPGC (1x genome coverage), CPM, RPKM, and BPM to ensure valid sample comparisons.

How does this skill assist with Quality Control?

It provides specific tools for correlation analysis, PCA, sequencing depth assessment, and fragment size validation to ensure data integrity.

What sequencing types does the deepTools skill support?

It is designed for high-throughput sequencing data including ChIP-seq, RNA-seq, ATAC-seq, and MNase-seq experiments.

Does it support automated workflow generation?

Yes, it includes a workflow generator that creates customized shell scripts for common analysis patterns like ChIP-seq QC and ATAC-seq processing.

deepTools NGS Analysis

Name: deepTools NGS Analysis
Author: Sologa

bySologa

データサイエンスとML

Analyzes and visualizes high-throughput sequencing data including ChIP-seq, RNA-seq, and ATAC-seq.

概要

deepTools is a comprehensive suite of Python tools designed for the complete NGS data analysis pipeline, from processing BAM files to generating publication-quality visualizations. It enables bioinformaticians to perform robust quality control, normalize coverage tracks, compare samples, and visualize genomic signal enrichment around features like TSS or peaks, supporting standardized and reproducible workflows for diverse sequencing experiments.

主な機能

Converts BAM alignments to normalized bigWig/bedGraph coverage tracks
Performs advanced QC including fingerprint plots, PCA, and correlation analysis
Supports specialized workflows for ChIP-seq, RNA-seq, and ATAC-seq
0 GitHub stars
Generates heatmaps and profile plots for genomic feature visualization
Provides automated file validation and workflow template generation

ユースケース

Generating normalized coverage tracks for visualization in genome browsers
Assessing the enrichment quality and reproducibility of ChIP-seq replicates
Visualizing signal intensity patterns around transcription start sites or genomic peaks

概要

主な機能

Converts BAM alignments to normalized bigWig/bedGraph coverage tracks
Performs advanced QC including fingerprint plots, PCA, and correlation analysis
Supports specialized workflows for ChIP-seq, RNA-seq, and ATAC-seq
0 GitHub stars
Generates heatmaps and profile plots for genomic feature visualization
Provides automated file validation and workflow template generation

ユースケース

Generating normalized coverage tracks for visualization in genome browsers
Assessing the enrichment quality and reproducibility of ChIP-seq replicates
Visualizing signal intensity patterns around transcription start sites or genomic peaks