DESCRIPTION

Package: oligoGames
Version: 0.1.0
Date: 2016-12-24
Type: Package
Title: Analyze data from massively parallel reporter assays
Authors@R: c(
    person("Chinmay", "Shukla", email = "cshukla@fas.harvard.edu", role = c("aut", "cre")), 
    person("Keegan", "Korthauer", email = "keegan@jimmy.harvard.edu", role = "aut"), 
    person("Rafael", "Irizarry", email = "rafa@jimmy.harvard.edu", role="aut"))
Maintainer: Chinmay Shukla <cshukla@fas.harvard.edu>
Description: 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.
Depends:
    R (>= 3.3.2)
Imports:
    bsseq (>= 1.10.0),
    bumphunter (>= 1.14.0),
    doParallel (>= 1.0.10),
    doRNG (>= 1.6),
    dplyr (>= 0.5.0),
    EBSeq (>= 1.14.0),
    foreach (>= 1.4.3),
    GenomicRanges (>= 1.26.1),
    iterators (>= 1.0.8),
    locfit (>= 1.5-9.1),
    reshape2 (>= 1.4.2),
    rPython (>= 0.0-6),
    splines (>= 3.3.2),
    tidyr (>= 0.6.0),
    utils (>= 3.3.2)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: testthat