Package: GenomicPlot 1.11.0

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 <[email protected]>

GenomicPlot_1.11.0.tar.gz
GenomicPlot_1.11.0.zip(r-4.7)GenomicPlot_1.11.0.zip(r-4.6)GenomicPlot_1.11.0.zip(r-4.5)
GenomicPlot_1.11.0.tgz(r-4.6-any)GenomicPlot_1.11.0.tgz(r-4.5-any)
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GenomicPlot_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GenomicPlot/json (API)

# Install 'GenomicPlot' in R:

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

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-1.11.0(bioc 3.24)GenomicPlot-1.10.0(bioc 3.23)

alternativesplicing chipseq coverage geneexpression rnaseq sequencing software transcription visualization annotation

5.48 score 6 stars 7 scripts 57 exports 209 dependencies

Last updated from:877256f4f4. Checks:1 WARNING, 4 NOTE, 2 OK, 3 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	319
linux-devel-x86_64	NOTE	785
source / vignettes	OK	490
linux-release-x86_64	NOTE	715
macos-release-arm64	NOTE	598
macos-oldrel-arm64	NOTE	401
windows-devel	ERROR	506
windows-release	ERROR	516
windows-oldrel	ERROR	510
wasm-release	OK	250

Exports:aov_TukeyHSD check_constraints custom_TxDb_from_GTF draw_boxplot_by_factor draw_boxplot_wo_outlier draw_combo_plot draw_locus_profile draw_matrix_heatmap draw_mean_se_barplot draw_quantile_plot draw_rank_plot draw_region_landmark draw_region_name draw_region_profile draw_stacked_plot draw_stacked_profile effective_size extract_longest_tx filter_by_nonoverlaps_stranded filter_by_overlaps_nonstranded filter_by_overlaps_stranded gene2tx get_genomic_feature_coordinates get_targeted_genes get_txdb_features gr2df handle_bam handle_bed handle_bedGraph handle_bw handle_input handle_wig make_subTxDb_from_GTF overlap_pair overlap_quad overlap_triple parallel_countOverlaps parallel_scoreMatrixBin plot_5parts_metagene plot_bam_correlation plot_locus plot_locus_with_random plot_overlap_bed plot_overlap_genes plot_peak_annotation plot_region plot_start_end plot_start_end_with_random prepare_3parts_genomic_features prepare_5parts_genomic_features process_scoreMatrix rank_rows rm_outlier set_seqinfo setImportParams start_parallel stop_parallel

Dependencies:abind AnnotationDbi askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob boot broom BSgenome BSgenome.Hsapiens.UCSC.hg19 bslib cachem car carData cigarillo circlize cli clipr clue cluster codetools colorspace ComplexHeatmap corrplot cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray Deriv digest doBy doParallel dplyr DT edgeR evaluate farver fastmap filelock fontawesome foreach forecast formatR Formula fracdiff fs futile.logger futile.options generics genomation GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggplot2 ggplotify ggpubr ggrepel ggsci ggsignif GlobalOptions glue gprofiler2 gridBase gridExtra gridGraphics gtable highr hms htmltools htmlwidgets httr httr2 impute IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma lme4 lmtest locfit magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr nlme nloptr nnet numDeriv openssl otel pbapply pbkrtest pheatmap pillar pkgconfig plotly plotrix plyr plyranges png polynom prettyunits progress promises proxy purrr quantreg R6 ranger rappdirs rbibutils RCAS RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack readr reformulas reshape2 restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rstatix rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo seqLogo seqPattern shape snow SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate tinytex txdbmaker tzdb UCSC.utils urca utf8 vctrs VennDiagram viridis viridisLite vroom withr xfun XML xml2 XVector yaml yulab.utils zoo

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

Rendered fromGenomicPlot_vignettes.rmdusingknitr::rmarkdown

Last update: 2025-12-08
Started: 2023-02-07

Help page	Topics
Perform one-way ANOVA and post hoc TukeyHSD tests	aov_TukeyHSD
Check constraints of genomic ranges	check_constraints
Make custom TxDb object from a GTF/GFF file	custom_TxDb_from_GTF
Plot boxplot with two factors	draw_boxplot_by_factor
Plot boxplot without outliers	draw_boxplot_wo_outlier
Make combo plot for statistics plots	draw_combo_plot
Plot signal profile around genomic loci	draw_locus_profile
Display matrix as a heatmap	draw_matrix_heatmap
Plot barplot for mean with standard error bars	draw_mean_se_barplot
Plot quantile over value	draw_quantile_plot
Plot fraction of cumulative sum over rank	draw_rank_plot
Plot genomic region landmark indicator	draw_region_landmark
Plot genomic region names	draw_region_name
Plot signal profile in genomic regions	draw_region_profile
draw stacked plot	draw_stacked_plot
Plot signal profile around start, center, and end of genomic regions	draw_stacked_profile
Normalize sample library size to effective size	effective_size
Toy data for examples and testing of the `GenomicPlot` package	chip_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 genes	extract_longest_tx
Filter GRanges by nonoverlaps in a stranded way	filter_by_nonoverlaps_stranded
Filter GRanges by overlaps in a nonstranded way	filter_by_overlaps_nonstranded
Filter GRanges by overlaps in a stranded way	filter_by_overlaps_stranded
Translate gene names to transcript ids using a GTF file for a subset of genes	gene2tx
GenomicPlot-package	GenomicPlot
Extract genomic features from TxDb object	get_genomic_feature_coordinates
Get the number of peaks overlapping each feature of all protein-coding genes	get_targeted_genes
Get genomic coordinates of features of protein-coding genes	get_txdb_features
Toy data for examples and testing of the `GenomicPlot` package	gf5_genomic
Toy data for examples and testing of the `GenomicPlot` package	gf5_meta
Convert GRanges to dataframe	gr2df
Handle files in bam format	handle_bam
Handle files in bed\|narrowPeak\|broadPeak format	handle_bed
Handle files in bedGraph format	handle_bedGraph
Handle files in bw\|bigwig\|bigWig\|BigWig\|BW\|BIGWIG format	handle_bw
Handle import of NGS data with various formats	handle_input
Handle files in wig format	handle_wig
Make TxDb object from a GTF file for a subset of genes	make_subTxDb_from_GTF
Plot two-sets Venn diagram	overlap_pair
Plot four-sets Venn diagram	overlap_quad
Plot three-sets Venn diagram	overlap_triple
Parallel execution of countOverlaps	parallel_countOverlaps
Parallel execution of scoreMatrixBin on a huge target windows object split into chunks	parallel_scoreMatrixBin
Plot promoter, 5'UTR, CDS, 3'UTR and TTS	plot_5parts_metagene
Plot correlation of bam files	plot_bam_correlation
Plot signal around custom genomic loci	plot_locus
Plot signal around custom genomic loci and random loci for comparison	plot_locus_with_random
Plot Venn diagrams depicting overlap of genomic regions	plot_overlap_bed
Plot Venn diagrams depicting overlap of gene lists	plot_overlap_genes
Annotate peaks with genomic features and genes	plot_peak_annotation
Plot signal inside as well as around custom genomic regions	plot_region
Plot signals around the start and the end of genomic features	plot_start_end
Plot signals around the start and the end of genomic features and random regions	plot_start_end_with_random
Demarcate genes into promoter, gene body and TTS features	prepare_3parts_genomic_features
Demarcate genes into promoter, 5'UTR, CDS, 3'UTR and TTS features	prepare_5parts_genomic_features
Preprocess scoreMatrix before plotting	process_scoreMatrix
Rank rows of a matrix based on user input	rank_rows
Remove outliers from scoreMatrix	rm_outlier
Set standard chromosome size of model organisms	set_seqinfo
set parameters for 'handle_input' function	setImportParams
Prepare for parallel processing	start_parallel
Stop parallel processing	stop_parallel
Toy data for examples and testing of the `GenomicPlot` package	txdb.sql

Package: GenomicPlot 1.11.0

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

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