%0 DATA
%A John, Smestad
%A L., Maher
%D 2015
%T Additional file 19: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription
%U https://springernature.figshare.com/articles/Additional_file_19_of_Relationships_between_putative_G-quadruplex-forming_sequences_RecQ_helicases_and_transcription/4467257
%R 10.6084/m9.figshare.c.3643949_D8.v1
%2 https://springernature.figshare.com/ndownloader/files/7196720
%K Additional
%K RecQ helicases
%K gene expression levels
%K FDR
%K bootstrapping simulations
%K gene expression
%K R 44 kb
%K G-quadruplex-forming sequences
%K gene sets
%K PQS position
%K regression model
%K PQS transcriptional effects
%K transcription R code
%K modeling prediction errors
%K epigenomic data
%X R code for implementing epigenetic modeling of gene expression and analyzing PQS transcriptional effects. Program written in R that takes Additional files 12, 13, 14, 15, 16, 17, 18 as inputs and trains a Bayesian linear regression model upon epigenomic data to predict gene expression levels. Models are then applied to gene sets not used for training, and the subsequent sorting of modeling prediction errors by PQS position is used to calculate PQS transcriptional effects. Also conducts statistical bootstrapping simulations to estimate the FDR for this analysis. (R 44 kb)