Welcome to MARIO tools’s documentation!



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  • Update “RNA_structure_prediction.py” function to allow output of JSON files for predicted structure and refined structure (predicted structure after providing single-strand offset information). The JSON output can be uploaded into RNA2D-browser (developed by Xiaopeng Zhu ) to show the Circos view of secondary structure and digested location distribution.
  • Add an API function to convert dot format of RNA secondary structure into several linked blocks. see “dot2block
  • new strong interaction list added based on whole RNA annotation using a FDR cutoff, and using ES-indirect (dual crosslinking) sample as control. See: resources, update in “Select_strongInteraction_pp.py” as well.
  • Add result resources for identified strong interactions in mouse E14 cells and MEF cells.
  • New function to generate heatmap for intra-RNA interactions: Plot_interaction_heatmap.py.
  • Add new function to find overlap between two interaction sets based on their RNA annotations, see: intersectInteraction_genePair.R.
  • Allow input of two genomic regions to visualize local interactions using -r option in “Plot_interaction.py” function
Version 0.3.2 (2014-05-07):
  • change the name into MARIO
  • In “Select_strongInteraction_pp.py” function, now annotations are updated after doing clustering and for strong interaction. The indexing of annotation files may take some time.
  • New “RNA_structure_prediction.py” function to refine RNA structure prediction based on empirical offset of free energies for single strand nucleotide.
New features in 0.3.1 (2014-05-02):
  • Add “–release” option in “split_partner.py” function. Allow a Type3 read-pair considered to be a “Paired” chimeric fragment even linker does not show up.
  • Fix bugs in “Select_strongInteraction_pp.py” function when the number of mapped pairs is low and some chromosomes don’t have any mapped read in part1 or part2.
  • Add bowtie 2 option and Unique-align option in “Stitch-seq_Aligner.py” function.
  • Different colors for different types of interactions in the visualization of interactome.
  • New API for folding energies of two RNA molecules, see “RNAstructure”.
  • Allow permutation-based strategies to calculate the p-value for the overlap between two independent interaction sets in “intersectInteraction.py” function
New features in 0.2.2:

Indices and tables