cshukla/oligoGames: Analyze data from massively parallel reporter assays

Analyze data from Massively Parallel Reporter Assays - MPRA's. Design an oligo pool by tiling a set of regions. Map the FASTQ files generated from the experiment back to the unique barcode for each oligo and generate a counts table for all the oligos. Normalize the counts table for library size using median or quantile normalization. Model nucleotide level counts from the oligo level counts using either the median, sum or PGM based on overlapping oligos. Perform inference on the nucleotide level counts and find differential regions by fitting splines, identifying bumps and subsequently shuffling the data to get FDRs.

install.packages("remotes")
remotes::install_github("cshukla/oligoGames")