Package: DiffBind
Type: Package
Version: 3.13.0
Title: Differential Binding Analysis of ChIP-Seq Peak Data
Authors@R: c(person("Rory","Stark", email="",
                  role = c("aut", "cre")),
Description: Compute differentially bound sites from multiple ChIP-seq
        experiments using affinity (quantitative) data. Also enables
        occupancy (overlap) analysis and plotting functions.
License: Artistic-2.0
LazyLoad: yes
Depends: R (>= 4.0), GenomicRanges, SummarizedExperiment
Imports: RColorBrewer, amap, gplots, grDevices, limma,
         GenomicAlignments, locfit, stats, utils, IRanges, lattice,
         systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel,
         S4Vectors, Rsamtools (>= 2.13.1), DESeq2, methods, graphics, ggrepel,
         apeglm, ashr, GreyListChIP
Suggests: BiocStyle, testthat, xtable,
          rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr,
          rtracklayer, grid
LinkingTo: Rhtslib (>= 1.99.1), Rcpp
SystemRequirements: GNU make
Collate: core.R parallel.R model.R counts.R contrast.R normalize.R
         analyze.R analyze_deseq2.R analyze_edgeR.R
         blacklist.R report.R plots.R plotProfile.R io.R helper.R
         utils.R RcppExports.R cpp_wrapper.R DBA.R
biocViews: Sequencing, ChIPSeq,ATACSeq, DNaseSeq, MethylSeq, RIPSeq,
           DifferentialPeakCalling, DifferentialMethylation, 
           GeneRegulation, HistoneModification,
           PeakDetection, BiomedicalInformatics, CellBiology,
           MultipleComparison, Normalization, ReportWriting, 
           Epigenetics, FunctionalGenomics