Analyzing eCLIP and iCLIP data with DEWSeq
Preface | Related packages | Acknowledgements | Introduction | Introduction to eCLIP sequencing | The idea behind DEWSeq | Understanding the signal | Binding modes | Chance of crosslinking | Background and antibodies | Enrichment of targets | Contaminants vs background | RNA fragment length and RNase concentrations | Read-throughs | Early truncations | Method | Differentially expressed sliding windows | Combining significant windows | Prerequisits for DEWSeq | Input controls | Replicates | Data pre-processing | Raw data pre-processing | Crosslink site extraction and counting | Detection of enriched regions with DEWSeq | Installation | Load the library | Importing data for DEWSeq | Read data | Estimating Size Factors | Prefiltering | DESeq2 approach | max window count approach | Estimate size factors based on a specific set of RNAs | Estimate size factor for assymetric data | Differential expressed windows analysis | Estimate dispersion | Call differentially bingind regions using wald test | Significance testing | Combining regions | Discussion | Session Info | References
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