Welcome to EPICC documentation!
A Snakemake-based pipeline for analyzing and integrating various types of (epi)genomics datasets, including histone and transcription factor ChIP-seq, RNA-seq, RAMPAGE, small RNA-seq, and methylC-seq.
Overview
EpigeneticButton is a comprehensive pipeline that processes and analyzes multiple types of genomics data. It provides an automated workflow for:
Data preprocessing and quality control
Read mapping and alignment
Peak calling and differential expression analysis
Data integration and visualization
Features
Multiple Data Types Support:
Histone ChIP-seq
Transcription Factor ChIP-seq
RNA-seq
small RNA-seq
MethylC-seq (mC)
RAMPAGE *in development
Automated Analysis:
Reference genome preparation
Sample-specific processing
Data type-specific analysis
Combined analysis across samples
Quality control and reporting
Additional output options such as heatmaps, metaplots and browsers
Flexible Configuration:
App to validate configuration options: epicc-builder
Customizable mapping parameters
Configurable analysis options
Resource management
Parallel processing
Contents
- Installation
- Configuration
- Usage
- Running the pipeline
- Intermediate Target Rules
- Additional Output Options
- Plotting RNAseq expression levels on target genes
- Performing GO analysis on target genes
- Finding motifs on target regions
- Performing sRNA differential analysis on target regions
- Plotting heatmap on target regions
- Plotting metaplot profiles on target regions
- Plotting browser screenshots on target regions
- Rerunning a specific analysis
- Output
- Help
- Credits