DESCRIPTION

Package: rgenie
Title: Analysis of GenIE Experiments
Version: 1.1.0
Authors@R: person("Jeremy", "Schwartzentruber", email = "jeremy37@gmail.com", role = c("aut", "cre"))
Description: The R package for GenIE analysis is designed to analyze the next-generation sequencing
    output from a set of GenIE experimental replicates. GenIE (genome-editing interrogation of enhancers)
    is an experimental method to evaluate the effects of individual single-nucleotide polymorphisms (SNPs)
    on gene transcription or on ATAC peaks. It is based on targeted CRISPR-Cas9 genome editing in cultured cells to
    produce indels at a target locus, optionally with a homology-dependent recombination (HDR) construct
    to create precisely defined genomic changes. For an RNA analysis, both genomic DNA (gDNA) and RNA are
    extracted from the same pool of cells, then complementary DNA (cDNA) is generated from the RNA. Both
    gDNA and cDNA are amplified with locus-specific PCR primers, in multiple replicates, and libraries of
    the experimental replicates are prepared for next-generation sequencing. The sequencing data from each
    replicate for each region should be aligned to either the full reference genome or to a locus-specific
    (amplicon) reference genome for analysis by 'rgenie'.
License: MIT + file LICENSE
URL: https://github.com/jeremy37/rgenie
BugReports: https://github.com/jeremy37/rgenie/issues
Encoding: UTF-8
LazyData: true
biocViews:
Imports:
    dplyr (>= 1.0.2),
    ggplot2 (>= 3.3.2),
    magrittr (>= 1.5),
    stringr (>= 1.4.0),
    readr (>= 1.3.1),
    tidyr (>= 1.1.2),
    tibble (>= 3.0.3),
    purrr (>= 0.3.4),
    forcats (>= 0.5.0),
    stats,
    cowplot (>= 0.9.4),
    egg (>= 0.4.2),
    ggdendro (>= 0.1-20),
    gridExtra (>= 2.3),
    FNN (>= 1.1.3),
    variancePartition (>= 1.14.0),
    Rsamtools (>= 2.0.0),
    IRanges (>= 2.18.1)
Suggests: 
    knitr,
    rmarkdown,
    devtools
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Depends: 
    R (>= 3.3)