# Plot profiles of next generation sequencing data in genomic features

## Documentation for package ‘GenomicPlot’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

aov_TukeyHSD | Perform one-way ANOVA and post hoc TukeyHSD tests
check_constraints | Check constraints of genomic ranges
chip_input_chr19.bam | Toy data for examples and testing of the 'GenomicPlot' package
chip_treat_chr19.bam | Toy data for examples and testing of the 'GenomicPlot' package
custom_TxDb_from_GTF | Make custom TxDb object from a GTF/GFF file
draw_boxplot_by_factor | Plot boxplot with two factors
draw_boxplot_wo_outlier | Plot boxplot without outliers
draw_combo_plot | Make combo plot for statistics plots
draw_locus_profile | Plot signal profile around genomic loci
draw_matrix_heatmap | Display matrix as a heatmap
draw_mean_se_barplot | Plot barplot for mean with standard error bars
draw_quantile_plot | Plot quantile over value
draw_rank_plot | Plot fraction of cumulative sum over rank
draw_region_landmark | Plot genomic region landmark indicator
draw_region_name | Plot genomic region names
draw_region_profile | Plot signal profile in genomic regions
draw_stacked_plot | draw stacked plot
draw_stacked_profile | Plot signal profile around start, center, and end of genomic regions
effective_size | Normalize sample library size to effective size
extdata | Toy data for examples and testing of the 'GenomicPlot' package
extract_longest_tx | Extract the longest transcript for each protein-coding genes
filter_by_nonoverlaps_stranded | Filter GRanges by nonoverlaps in a stranded way
filter_by_overlaps_nonstranded | Filter GRanges by overlaps in a nonstranded way
filter_by_overlaps_stranded | Filter GRanges by overlaps in a stranded way
gencode.v19.annotation_chr19.gtf | Toy data for examples and testing of the 'GenomicPlot' package
gene2tx | Translate gene names to transcript ids using a GTF file for a subset of genes
GenomicPlot | GenomicPlot-package
get_genomic_feature_coordinates | Extract genomic features from TxDb object
get_targeted_genes | Get the number of peaks overlapping each feature of all protein-coding genes
get_txdb_features | Get genomic coordinates of features of protein-coding genes
gf5_genomic | Toy data for examples and testing of the 'GenomicPlot' package
gf5_meta | Toy data for examples and testing of the 'GenomicPlot' package
gr2df | Convert GRanges to dataframe
handle_bam | Handle files in bam format
handle_bed | Handle files in bed|narrowPeak|broadPeak format
handle_bedGraph | Handle files in bedGraph format
handle_bw | Handle files in bw|bigwig|bigWig|BigWig|BW|BIGWIG format
handle_input | Handle import of NGS data with various formats
handle_wig | Handle files in wig format
input_chr19.bam | Toy data for examples and testing of the 'GenomicPlot' package
make_subTxDb_from_GTF | Make TxDb object from a GTF file for a subset of genes
overlap_pair | Plot two-sets Venn diagram
overlap_quad | Plot four-sets Venn diagram
overlap_triple | Plot three-sets Venn diagram
parallel_countOverlaps | Parallel execution of countOverlaps
parallel_scoreMatrixBin | Parallel execution of scoreMatrixBin on a huge target windows object split into chunks
plot_5parts_metagene | Plot promoter, 5'UTR, CDS, 3'UTR and TTS
plot_bam_correlation | Plot correlation of bam files
plot_locus | Plot signal around custom genomic loci
plot_locus_with_random | Plot signal around custom genomic loci and random loci for comparison
plot_overlap_bed | Plot Venn diagrams depicting overlap of genomic regions
plot_overlap_genes | Plot Venn diagrams depicting overlap of gene lists
plot_peak_annotation | Annotate peaks with genomic features and genes
plot_region | Plot signal inside as well as around custom genomic regions
plot_start_end | Plot signals around the start and the end of genomic features
plot_start_end_with_random | Plot signals around the start and the end of genomic features and random regions
prepare_3parts_genomic_features | Demarcate genes into promoter, gene body and TTS features
prepare_5parts_genomic_features | Demarcate genes into promoter, 5'UTR, CDS, 3'UTR and TTS features
process_scoreMatrix | Preprocess scoreMatrix before plotting
rank_rows | Rank rows of a matrix based on user input
rm_outlier | Remove outliers from scoreMatrix
setImportParams | set parameters for 'handle_input' function
set_seqinfo | Set standard chromosome size of model organisms
start_parallel | Prepare for parallel processing
stop_parallel | Stop parallel processing
test_chip_peak_chr19.bed | Toy data for examples and testing of the 'GenomicPlot' package
test_chip_peak_chr19.narrowPeak | Toy data for examples and testing of the 'GenomicPlot' package
test_chr19.bedGraph | Toy data for examples and testing of the 'GenomicPlot' package
test_clip_peak_chr19.bed | Toy data for examples and testing of the 'GenomicPlot' package
test_file1.txt | Toy data for examples and testing of the 'GenomicPlot' package
test_file2.txt | Toy data for examples and testing of the 'GenomicPlot' package
test_file3.txt | Toy data for examples and testing of the 'GenomicPlot' package
test_file4.txt | Toy data for examples and testing of the 'GenomicPlot' package
test_wig_chr19_+.bw | Toy data for examples and testing of the 'GenomicPlot' package
test_wig_chr19_+.wig | Toy data for examples and testing of the 'GenomicPlot' package
treat_chr19.bam | Toy data for examples and testing of the 'GenomicPlot' package
txdb.sql | Toy data for examples and testing of the 'GenomicPlot' package