Package: GenomicPlot
Type: Package
Title: Plot profiles of next generation sequencing data in genomic
        features
Version: 1.4.0
Authors@R: person("Shuye", "Pu", email = "shuye2009@gmail.com", role = c("aut", "cre"), 
   comment = c(ORCID = "0000-0002-6664-8438"))
Description: Visualization of next generation sequencing (NGS) data is essential 
   for interpreting high-throughput genomics experiment results. 'GenomicPlot' 
   facilitates plotting of NGS data in various formats (bam, bed, wig and bigwig);
   both coverage and enrichment over input can be computed and displayed with 
   respect to genomic features (such as UTR, CDS, enhancer), and user defined 
   genomic loci or regions. Statistical tests on signal intensity within user 
   defined regions of interest can be performed and represented as boxplots or 
   bar graphs. Parallel processing is used to speed up computation on multicore 
   platforms. In addition to genomic plots which is suitable for displaying of 
   coverage of genomic DNA (such as ChIPseq data), metagenomic (without introns) 
   plots can also be made for RNAseq or CLIPseq data as well. 
License: GPL-2
Encoding: UTF-8
LazyData: FALSE
Collate: "DrawingFunctions.R" "GenomicPlot.R" "HandleDataMatrix.R"
        "HandleFeatures.R" "Parallel.R" "ReadData.R" "Setup.R"
        "Plot_5parts_metagene.R" "Plot_start_end.R"
        "Plot_start_end_with_random.R" "Plot_region.R" "Plot_locus.R"
        "data.R" "Plot_locus_with_random.R" "Plot_peak_annotation.R"
        "Plot_bam_correlation.R"
Depends: R (>= 4.4.0), GenomicRanges (>= 1.46.1)
Imports: methods, Rsamtools, parallel, tidyr, rtracklayer (>= 1.54.0),
        plyranges (>= 1.14.0), cowplot (>= 1.1.1), VennDiagram,
        ggplotify, GenomeInfoDb, IRanges, ComplexHeatmap, RCAS (>=
        1.20.0), scales (>= 1.2.0), GenomicAlignments (>= 1.30.0),
        edgeR, circlize, viridis, ggsignif (>= 0.6.3), ggsci (>= 2.9),
        ggpubr, grDevices, graphics, stats, utils, GenomicFeatures,
        genomation (>= 1.36.0), txdbmaker, ggplot2 (>= 3.3.5),
        BiocGenerics, dplyr, grid
Suggests: knitr, rmarkdown, R.utils, Biobase, BiocStyle, testthat,
        AnnotationDbi
biocViews: AlternativeSplicing, ChIPSeq, Coverage, GeneExpression,
        RNASeq, Sequencing, Software, Transcription, Visualization,
        Annotation
RoxygenNote: 7.3.1
VignetteBuilder: knitr
BugReports: https://github.com/shuye2009/GenomicPlot/issues
URL: https://github.com/shuye2009/GenomicPlot
git_url: https://git.bioconductor.org/packages/GenomicPlot
git_branch: RELEASE_3_20
git_last_commit: 6b50b97
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
NeedsCompilation: no
Packaged: 2024-10-30 03:05:40 UTC; biocbuild
Author: Shuye Pu [aut, cre] (<https://orcid.org/0000-0002-6664-8438>)
Maintainer: Shuye Pu <shuye2009@gmail.com>
Built: R 4.4.1; ; 2024-10-30 15:57:53 UTC; windows
