NSMB Tutorials are now available under the 'tutorials' folder as RMarkdown files. The HTML workflows for protein-protein interactions and protein-RNA interactions are available via the links provided.
This package is designed to analyze and visualize crosslinking (XL) data from multiple sources (mainly XL-MS and RBDmap).
Analysis
-
Differential analysis
-
Crosslinking frequency
-
Creation of PDB files for missing peptides
-
Mutation and Uniprot Integration (coming soon!)
XL-MS
- Control distances for PDB structures
RBDMap
- Frequency of RNA-likened amino acids
Visualization
-
Distance histograms
-
Amino acid frequency heatmaps
-
2D: xiNET output
-
3D: PyMOL output
Installation
To download the functions with documentation:
library('devtools')
install_github("egmg726/crisscrosslinker")Note
This is still the beta release of the package/documentation so please contact me if you come across any issues!