DESCRIPTION

Package: ATACseqQCWorkshop
Title: Best practices for ATAC-seq QC and data analysis
Version: 0.1.0
Authors@R: 
    c(person(given = "Haibo",
           family = "Liu",
           role = c("aut", "cre"),
           email = "haibo.liu@umassmed.edu"),
    person(given = "Jianhong",
            family = "Ou",
            role = c("aut"),
            email = "jianhong.ou@duke.edu"),
    person(given = "Kai",
            family = "Hu",
            role = c("aut"),
            email = "Kai.Hu@umassmed.edu"),
    person(given = "Lihua",
            family = "Zhu",
            role = c("aut"),
            email = "Julie.Zhu@umassmed.edu"))
Description: ATAC-seq, an assay for Transposase-Accessible Chromatin
    using sequencing, is a rapid and sensitive method for chromatin
    accessibility analysis. Compared to other methods, such as 
    MNase-seq, FAIRE-seq and DNAse-seq, ATAC-seq requires less 
    biological materials and time to process. In this workshop, 
    participants will not only gain the theoretical understanding of
    the characteristics of ATAC-seq data and the workflow of ATAC-seq
    data quality assessment, but will also obtain hands-on experience
    in analyzing ATAC-seq data using the ATACseqQC package. We will
    provide a brief introduction to the ATAC-seq technology, high
    quality data generation and computational analysis workflow. Then, 
    we will give a demo to perform a comprehensive quality assessment
    of a typical ATAC-seq dataset using the ATACseqQC package. Participants 
    will have the opportunity to analyze several excerpted datasets of 
    different quality. Detailed notes and R code will be provided for
    reproducibility and follow-up practicing.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.0
Depends: R (>= 4.0), ATACseqQC, Biobase
Suggests: knitr, rmarkdown, pkgdown, BiocGenerics, S4Vectors, BSgenome, Biostrings,
    ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, 
    GenomicScores, graphics, grid, limma, Rsamtools (>= 1.31.2), randomForest,
    rtracklayer, stats, motifStack, preseqR, utils, KernSmooth, edgeR, BiocStyle,
    BSgenome.Hsapiens.UCSC.hg38,TxDb.Hsapiens.UCSC.hg38.knownGene, 
    BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, 
    MotifDb, trackViewer, SRAdb, png, jpeg
URL: https://haibol2016.github.io/ATACseqQCWorkshop/
BugReports: https://github.com/haibol2016/ATACseqQCWorkshop/issues/new/choose
VignetteBuilder: knitr
DockerImage: nemat1976/atacseqqcworkshop_2020:latest