DESCRIPTION

Package: preciseTADworkshop
Title: A workshop describing preciseTAD: A machine learning framework for 
    precise 3D domain boundary prediction at base-level resolution
Version: 0.1.1
Authors@R: c(
    person(given = "Spiro",
           family = "Stilianoudakis",
           role = c("aut", "cre"),
           email = "stilianoudasc@vcu.edu"),
    person(given = "Mikhail",
           family = "Dozmorov",
           role = c("aut"),
           email = "mikhail.dozmorov@gmail.com",
           comment = c(ORCID = "0000-0002-0086-8358")))
Description: Chromosome conformation capture technologies combined with
    high-throughput sequencing (Hi-C) have revealed that chromatin undergoes 
    layers of compaction through DNA looping and folding, forming dynamic 3D 
    structures. Among these are Topologically Associating Domains (TADs), which 
    are known to play critical roles in cell dynamics like gene regulation and 
    cell differentiation. Precise identification of TAD boundaries (TAD-calling)
    remains difficult, as it is strongly reliant on Hi-C data resolution. 
    Obtaining genome-wide chromatin interactions at high-resolution is costly 
    resulting in low resolution of Hi-C matrices and high uncertainty in the 
    location of domain boundaries. In this workshop, we will introduce a novel 
    approach for transforming TAD-calling into a supervised machine learning 
    framework using functional genomic elements. We will walk the user through
    the customizable model building process and finish with an application of
    precisely predicting boundaries at base-level resolution. The methods 
    demonstrated in this workshop are from the `preciseTAD` R package.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.0
Depends: 
    Biobase,
    R (>= 4.0.0)
Suggests: 
    knitr,
    rmarkdown,
    pkgdown
Imports: 
    devtools,
    ExperimentHub,
    preciseTAD,
    S4Vectors,
    IRanges,
    GenomicRanges,
    randomForest,
    ModelMetrics,
    e1071,
    PRROC,
    pROC,
    caret,
    DMwR,
    utils,
    cluster,
    dbscan,
    doSNOW,
    foreach,
    pbapply,
    stats,
    parallel
URL: https://dozmorovlab.github.io/preciseTADworkshop/
BugReports: https://github.com/mdozmorov/preciseTADworkshop/issues/new/choose
VignetteBuilder: knitr
DockerImage: stilianoudakis/precisetadworkshop:latest