Package: chipseqDB
Title: From reads to regions: a Bioconductor workflow to detect
        differential binding in ChIP-seq data
Version: 1.2.0
Date: 2018-04-26
Authors@R: c(person(role=c("aut","cre"), "Aaron", "Lun", email = "alun@wehi.edu.au"),
             person(role="aut", "Gordon ", "Smyth", email = "smyth@wehi.edu.au"))
Description: This article describes a computational workflow for performing a DB analysis with sliding windows.
    The aim is to facilitate the practical implementation of window-based DB analyses by providing detailed code
    and expected output. The workflow described here applies to any ChIP-seq experiment with multiple experimental
    conditions and with multiple biological samples within one or more of the conditions. It detects and summarizes
    DB regions between conditions in a *de novo* manner, i.e., without making any prior assumptions about the location
    or width of bound regions.Detected regions are then annotated according to their proximity to annotated genes.
    In addition, the code can be easily adapted to accommodate batch effects, covariates and multiple experimental factors.
Depends: R (>= 3.3.0), BiocStyle, ChIPpeakAnno, Gviz, Rsamtools,
        Rsubread, TxDb.Mmusculus.UCSC.mm10.knownGene, csaw, edgeR,
        knitr, locfit, org.Mm.eg.db, rtracklayer, statmod
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
biocViews: Workflow, EpigeneticsWorkflow
Workflow: true
Suggests: knitr, rmarkdown
NeedsCompilation: no
URL: https://www.bioconductor.org/help/workflows/chipseqDB/
Packaged: 2018-05-02 12:32:12 UTC; biocbuild
Author: Aaron Lun [aut, cre],
  Gordon Smyth [aut]
Maintainer: Aaron Lun <alun@wehi.edu.au>
