Package: chipseqDB
Title: From reads to regions: a Bioconductor workflow to detect
        differential binding in ChIP-seq data
Version: 1.4.1
Date: 2018-10-09
Authors@R: c(person(role=c("aut","cre"), "Aaron", "Lun", email = "infinite.monkeys.with.keyboards@gmail.com"),
        person(role="aut", "Gordon ", "Smyth"))
Description: 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 multiple biological samples in 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: ImmunoOncologyWorkflow, Workflow, EpigeneticsWorkflow
Workflow: true
Suggests: knitr, rmarkdown
NeedsCompilation: no
URL: https://www.bioconductor.org/help/workflows/chipseqDB/
git_url: https://git.bioconductor.org/packages/chipseqDB
git_branch: RELEASE_3_8
git_last_commit: 6f5d3ba
git_last_commit_date: 2019-01-08
Date/Publication: 2019-01-09
Packaged: 2019-01-09 14:28:42 UTC; biocbuild
Author: Aaron Lun [aut, cre],
  Gordon Smyth [aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
