Introduction | Installation | Importing Hi-C data | Tabular files | Cooler files | Juicer files | HiC-Pro files | Running the HiCDOC pipeline | Filtering data | Normalizing biases | Technical biases | Biological biases | Distance effect | Predicting compartments and differences | Visualizing data and results | Sanity checks | PCA checks | Compartment assignemnt | Warnings | Session info | References

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

Rmmquant in a nutshell | Package | Inputs | Annotation | Annotation file | Annotation structure | Reads files | Outputs | Counts | Statistics | Options | Count matrix options | Row names | Column names | Input options | Library type | Reads file format. | Read assignement options | Overlap options | Read mapping to several features. | Row count options | Count threshold | Merge threshold | Use cases | Extracting GenomicRanges from Annotation Database | Using DESeq2 | Troubleshooting | Session information | References