Code to accompany the paper Chiang, Timothy; Kimchi, Ofer; Dhaliwal, Herman K.; Villarreal, Daniel A.; Vasquez, Fernando F.; Manoharan, Vinothan; Brenner, Michael P; Garmann, Rees; "Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays", Nucleic Acids Research 2025.
matlab_feature_extraction contains Matlab code to extracting integrated
fluorescence intensities from a raw microarray image.
microarray_design contains Matlab code to generate probe sequences and layouts
for DNA microarrays.
automated_microarray_design.ipynb is a Jupyter notebook that automates the
design of DNA microarrays for RNA structure analysis.
patchprobe is a python package for analysis of patch-probe microarray data.
See the file environment.yml for instructions on how to set up the conda
environment for running the code. See example-analysis-notebook.ipynb for a
demonstration of how to use the package.