"Finding differentially expressed unannotated genomic regions from RNA-seq data with srnadiff"
Version info | Abstract | Introduction | Citing r Biocpkg("srnadiff") | How to get help for r Biocpkg("srnadiff") | Quick start | Using r Biocpkg("srnadiff") | Installation | Data overview | Data preparation: the srnadiffExp object | Content | Adding an annotation | Directionality | The srnaExp object | Read annotation | Extraction of putative regions using an GTF annotation file | Whole genome file annotation | Extraction of precursor miRNAs using a miRBase-formatted GFF file | Extraction of mature miRNAs using a miRBase-formatted GFF file | Other format | Performing sRNA-diff | Working with the srnadiffExp object | Extracting regions | Data visualization | Methods behind r Biocpkg("srnadiff") | Pre-processing data | Methods to produce differentially expressed regions | HMM method: hmm | IR method: IR | Naive method: naive | Quantifying DERs | General parameters | Combination of strategies | Choice of the strategies | Quantification of the features | Using an other method to compute adjusted p-values | Misc | Using several cores | Troubleshooting | Session information | References
Rendered fromsrnadiff.Rmdusingknitr::rmarkdown