Package: GenomicPlot 1.5.0

Shuye Pu

GenomicPlot: Plot profiles of next generation sequencing data in genomic features

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.

Authors:Shuye Pu [aut, cre]

GenomicPlot_1.5.0.tar.gz
GenomicPlot_1.5.0.zip(r-4.5)GenomicPlot_1.5.0.zip(r-4.4)GenomicPlot_1.3.4.zip(r-4.3)
GenomicPlot_1.5.0.tgz(r-4.4-any)GenomicPlot_1.3.4.tgz(r-4.3-any)
GenomicPlot_1.5.0.tar.gz(r-4.5-noble)GenomicPlot_1.5.0.tar.gz(r-4.4-noble)
GenomicPlot_1.5.0.tgz(r-4.4-emscripten)GenomicPlot_1.3.4.tgz(r-4.3-emscripten)
GenomicPlot.pdf |GenomicPlot.html✨
GenomicPlot/json (API)
NEWS

# Install 'GenomicPlot' in R:
install.packages('GenomicPlot', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/shuye2009/genomicplot/issues

Datasets:
  • gf5_genomic - Toy data for examples and testing of the 'GenomicPlot' package
  • gf5_meta - Toy data for examples and testing of the 'GenomicPlot' package

On BioConductor:GenomicPlot-1.3.4(bioc 3.20)GenomicPlot-1.2.4(bioc 3.19)

alternativesplicingchipseqcoveragegeneexpressionrnaseqsequencingsoftwaretranscriptionvisualizationannotation

5.71 score 3 stars 4 scripts 162 downloads 57 exports 200 dependencies

Last updated 20 days agofrom:6daf52b886. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winNOTESep 18 2024
R-4.3-macNOTESep 18 2024

Exports:aov_TukeyHSDcheck_constraintscustom_TxDb_from_GTFdraw_boxplot_by_factordraw_boxplot_wo_outlierdraw_combo_plotdraw_locus_profiledraw_matrix_heatmapdraw_mean_se_barplotdraw_quantile_plotdraw_rank_plotdraw_region_landmarkdraw_region_namedraw_region_profiledraw_stacked_plotdraw_stacked_profileeffective_sizeextract_longest_txfilter_by_nonoverlaps_strandedfilter_by_overlaps_nonstrandedfilter_by_overlaps_strandedgene2txget_genomic_feature_coordinatesget_targeted_genesget_txdb_featuresgr2dfhandle_bamhandle_bedhandle_bedGraphhandle_bwhandle_inputhandle_wigmake_subTxDb_from_GTFoverlap_pairoverlap_quadoverlap_tripleparallel_countOverlapsparallel_scoreMatrixBinplot_5parts_metageneplot_bam_correlationplot_locusplot_locus_with_randomplot_overlap_bedplot_overlap_genesplot_peak_annotationplot_regionplot_start_endplot_start_end_with_randomprepare_3parts_genomic_featuresprepare_5parts_genomic_featuresprocess_scoreMatrixrank_rowsrm_outlierset_seqinfosetImportParamsstart_parallelstop_parallel

Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbootbroomBSgenomeBSgenome.Hsapiens.UCSC.hg19bslibcachemcarcarDatacirclizeclicliprclueclustercodetoolscolorspaceComplexHeatmapcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDerivdigestdoBydoParalleldplyrDTedgeRevaluatefansifarverfastmapfilelockfontawesomeforeachformatRFormulafsfutile.loggerfutile.optionsgenericsgenomationGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2ggplotifyggpubrggrepelggsciggsignifGlobalOptionsgluegprofiler2gridBasegridExtragridGraphicsgtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2imputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalme4locfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpbapplypbkrtestpheatmappillarpkgconfigplogrplotlyplotrixplyrplyrangespngpolynomprettyunitsprogresspromisesproxypurrrquantregR6rangerrappdirsRCASRColorBrewerRcppRcppEigenRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLiterstatixrtracklayerS4ArraysS4VectorssassscalesseqLogoseqPatternshapesnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytextxdbmakertzdbUCSC.utilsutf8vctrsVennDiagramviridisviridisLitevroomwithrxfunXMLxml2XVectoryamlyulab.utilszlibbioc

GenomicPlot: an R package for efficient and flexible visualization of genome-wide NGS coverage profiles

Shuye Pu

Rendered fromGenomicPlot_vignettes.rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-01-08
Started: 2023-02-07

Readme and manuals

Help Manual

Help pageTopics
Perform one-way ANOVA and post hoc TukeyHSD testsaov_TukeyHSD
Check constraints of genomic rangescheck_constraints
Make custom TxDb object from a GTF/GFF filecustom_TxDb_from_GTF
Plot boxplot with two factorsdraw_boxplot_by_factor
Plot boxplot without outliersdraw_boxplot_wo_outlier
Make combo plot for statistics plotsdraw_combo_plot
Plot signal profile around genomic locidraw_locus_profile
Display matrix as a heatmapdraw_matrix_heatmap
Plot barplot for mean with standard error barsdraw_mean_se_barplot
Plot quantile over valuedraw_quantile_plot
Plot fraction of cumulative sum over rankdraw_rank_plot
Plot genomic region landmark indicatordraw_region_landmark
Plot genomic region namesdraw_region_name
Plot signal profile in genomic regionsdraw_region_profile
draw stacked plotdraw_stacked_plot
Plot signal profile around start, center, and end of genomic regionsdraw_stacked_profile
Normalize sample library size to effective sizeeffective_size
Toy data for examples and testing of the `GenomicPlot` packagechip_input_chr19.bam chip_treat_chr19.bam extdata gencode.v19.annotation_chr19.gtf input_chr19.bam test_chip_peak_chr19.bed test_chip_peak_chr19.narrowPeak test_chr19.bedGraph test_clip_peak_chr19.bed test_file1.txt test_file2.txt test_file3.txt test_file4.txt test_wig_chr19_+.bw test_wig_chr19_+.wig treat_chr19.bam
Extract the longest transcript for each protein-coding genesextract_longest_tx
Filter GRanges by nonoverlaps in a stranded wayfilter_by_nonoverlaps_stranded
Filter GRanges by overlaps in a nonstranded wayfilter_by_overlaps_nonstranded
Filter GRanges by overlaps in a stranded wayfilter_by_overlaps_stranded
Translate gene names to transcript ids using a GTF file for a subset of genesgene2tx
GenomicPlot-packageGenomicPlot
Extract genomic features from TxDb objectget_genomic_feature_coordinates
Get the number of peaks overlapping each feature of all protein-coding genesget_targeted_genes
Get genomic coordinates of features of protein-coding genesget_txdb_features
Toy data for examples and testing of the `GenomicPlot` packagegf5_genomic
Toy data for examples and testing of the `GenomicPlot` packagegf5_meta
Convert GRanges to dataframegr2df
Handle files in bam formathandle_bam
Handle files in bed|narrowPeak|broadPeak formathandle_bed
Handle files in bedGraph formathandle_bedGraph
Handle files in bw|bigwig|bigWig|BigWig|BW|BIGWIG formathandle_bw
Handle import of NGS data with various formatshandle_input
Handle files in wig formathandle_wig
Make TxDb object from a GTF file for a subset of genesmake_subTxDb_from_GTF
Plot two-sets Venn diagramoverlap_pair
Plot four-sets Venn diagramoverlap_quad
Plot three-sets Venn diagramoverlap_triple
Parallel execution of countOverlapsparallel_countOverlaps
Parallel execution of scoreMatrixBin on a huge target windows object split into chunksparallel_scoreMatrixBin
Plot promoter, 5'UTR, CDS, 3'UTR and TTSplot_5parts_metagene
Plot correlation of bam filesplot_bam_correlation
Plot signal around custom genomic lociplot_locus
Plot signal around custom genomic loci and random loci for comparisonplot_locus_with_random
Plot Venn diagrams depicting overlap of genomic regionsplot_overlap_bed
Plot Venn diagrams depicting overlap of gene listsplot_overlap_genes
Annotate peaks with genomic features and genesplot_peak_annotation
Plot signal inside as well as around custom genomic regionsplot_region
Plot signals around the start and the end of genomic featuresplot_start_end
Plot signals around the start and the end of genomic features and random regionsplot_start_end_with_random
Demarcate genes into promoter, gene body and TTS featuresprepare_3parts_genomic_features
Demarcate genes into promoter, 5'UTR, CDS, 3'UTR and TTS featuresprepare_5parts_genomic_features
Preprocess scoreMatrix before plottingprocess_scoreMatrix
Rank rows of a matrix based on user inputrank_rows
Remove outliers from scoreMatrixrm_outlier
Set standard chromosome size of model organismsset_seqinfo
set parameters for 'handle_input' functionsetImportParams
Prepare for parallel processingstart_parallel
Stop parallel processingstop_parallel
Toy data for examples and testing of the `GenomicPlot` packagetxdb.sql