James Dalgleish
Jan 29, 2026
basepairC is a package analyzing the highest resolution contact data available: Micro-Capture-C at ~1-6bp basepair resolution. This is several orders of magnitude smaller than even microC, and enables the 3D characterization finer than even a transcription factor binding site in a promoter. basepairC is a package for importing, correcting, and preprocessing these data to create 2D data structures ready for analysis, performing MNase bias correction, segmentation, and region-based statistical testing. The newest version of the package suite will be found here (in development): basepairC.core
To install the package, you can use the following command in R:
#install remotes if you haven't already
# install.packages("remotes")
remotes::install_github("jamesdalg/basepairC",dependencies=TRUE)Before beginning the tutorial for basepairC, be sure to make the core matrices in the basepairC tutorial. You can view the tutorial here: A quick test of baseapirC
You can also view the vignette in RStudio by running:
browseVignettes("basepairC")