seqPatch

R package detecting DNA modifications by kinetic data of SMRT sequencing

System requirement

Linux system. >=32Gb RAM is highly recommanded.

Pre-requisition

seqPatch depends on Rcpp and pbh5. User need to install them first.

Install Rcpp

launch R console and type

install.packages('Rcpp', dependencies=TRUE)

Install pbh5

https://github.com/PacificBiosciences/R-pbh5

Install seqPatch

R CMD INSTALL downloaded_folder_name

Reference

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002935

A real example

https://xfengz02.u.hpc.mssm.edu/example_release.tar.gz

The example implements "Detecting DNA modifications in E.coli K-12" section in the reference

Upcoming features

1. Estimating proportion of modifiled DNA molecules at a given genome loci.
2. Empirical Bayesian FDR estimation.