Package index

Violin plots

Compare log2FC or normalized counts between chromosomes.

violin_log2FC()

A function to generate violin-box plot to compare binding changes (log2FoldChange) between chromosome X and autosomes (A) based on ChIPseq data It also performs a t-test to assess statistical significance.

violin_counts()

Creates violin-box plots to compare normalized binding counts values between different conditions and chromosomes, typically comparing X chromosome vs autosomes.

violin_log2FC_all_chr()

Violin + box plot for all chromosomes separately (log2 fold change)

violin_counts_all_chr()

Violin + box plot for all chromosomes separately (normalized binding counts)

T-test scatter plots

Chromosome-level significance plots.

ttest_scatter()

Dot plot of -log10(p-value) for log2 fold-change comparisons along chromosomes

Diagnostic plots

MD plot and distribution plots for DiffBind output.

plot_md()

MA / MD plot for differential binding results

plot_distributions()

Density or histogram of normalized binding counts per chromosome

Peak utilities

Genomic overlap detection and visualization.

find_overlap_peaks()

Find overlapping peaks between two peak sets

upset_peaks()

UpSet plot for peak category overlaps

Example data

Built-in dataset for examples.

example_peaks

Example ChIP-seq differential binding peaks