DESCRIPTION

Package: workshop2020
Type: Package
Title: Basic and advanced bioinformatics for RegenerationNEXT
Version: 0.1.3
Author: Jianhong Ou
Maintainer: Jianhong Ou <jianhong.ou@duke.com>
Description: With breakthroughs in Next Generation Sequencing (NGS), 
    we are collecting vast amounts of data that will be analyzed for screening
    interesting targets. The details of these data reveal basic information 
    in genome-wide such as gene expression profiles, DNA-protein interactions,
    DNA-DNA interactions and chromatin structures, or may lead us to major 
    discoveries like gene-regeneration associations. This workshop is designed
    for postdoc, graduated students to get the basic and advanced bioinformatics
    skills used in RNA-seq and DNA-seq data analysis. We will focus on the 
    fundamentals of sequence analysis and try to let every attendance run 
    the pipeline with sample data in order to make researchers confident 
    in sequencing data analysis, understanding the results and presenting the 
    data by themselves. 
Depends:
    R (>= 3.6)
Imports:
    ade4,
    AnnotationHub,
    ATACseqQC,
    biomaRt,
    BiocManager,
    Biostrings,
    bookdown,
    BSgenome.Hsapiens.UCSC.hg19,
    BSgenome.Hsapiens.UCSC.hg38,
    ChIPpeakAnno,
    colorBlindness,
    dagLogo,
    EnsDb.Hsapiens.v75,
    GenomicFeatures,
    ggplot2,
    GO.db,
    jpeg,
    kableExtra,
    knitr,
    motifStack,
    MotifDb,
    org.Hs.eg.db,
    org.Mm.eg.db,
    pander, 
    pkgdown,
    png,
    RColorBrewer,
    reactome.db,
    Rsamtools,
    rtracklayer,
    seqinr,
    trackViewer,
    rmarkdown,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    UpSetR,
    VariantAnnotation,
    WriteXLS
License: MIT + file LICENSE
LazyData: TRUE
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Encoding: UTF-8
biocViews: Sequencing, GeneRegulation, QualityControl
URL: https://jianhong.github.io/workshop2020
BugReports: https://github.com/jianhong/workshop2020/issues/new/choose