The COMRADES experiment | rnaCrosslink data pre-processing | Nextflow pipeline | Nextflow pipeline output | Input for rnaCrosslink-OO | Load the Library | Make the Sample table | Choose RNA | Transript fasta | A set of interactions to compare to (optional) | Reactivities (optional) | Slow Start | rnaCrosslinkQC | Make the Object | Slots / Attributes | Analysis stage | Meta-data | Raw-data and processed data | rnaCrosslinkDataSet - make object | Access the data within the instance | General Acessors | Check Status of Instance | Retreive RNA Size | Retreive Meta-data | Retreive Sample Groups | Retreive Sample Names | Retreive Data in original format | Retreive Contact Matrices | Get Data | Check Interactions | topTranscripts | topInteractors | topInteractions | Get Count Matricies | Clustering | Cluster Numbers | Read numbers in clusters | Cluster Tables | Cluster GRanges | Cluster Trimming | Check Cluster Agreement between replicates | Folding | Other Plots and Functionality | Plotting contact matrices | Identifying domains | Analyse folds | Ensemble Stats | HotSpots of difference | PCA of ensembl | Plot to strcutures on an arc diagram | Plot one structure | Inter RNA interactions- Plot an interacting partner | Compare to the "Known" structure | Make a contact matrix of known / comprative interactions | Compare the Clusters | Plot the overlapping clusters | Compare structures with a set of contacts | Quick start