GenomicPlot             GenomicPlot-package
aov_TukeyHSD            Perform one-way ANOVA and post hoc TukeyHSD
                        tests
check_constraints       Check constraints of genomic ranges
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
gene2tx                 Translate gene names to transcript ids using a
                        GTF file for a subset of genes
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
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
txdb.sql                Toy data for examples and testing of the
                        'GenomicPlot' package
