Function reference • TOP

All functions
`add_chip_peak_labels_to_sites()`	Adds ChIP-seq peak labels to the candidate sites
`add_chip_signals_to_sites()`	Adds ChIP-seq signals to the candidate sites
`assemble_training_data()`	Assembles TOP training data for all TF x cell type combinations, then split training data into 10 partitions
`bin_transform_counts()`	Bins and transforms count matrix
`combine_TOP_samples()`	Combines and takes the average of TOP posterior samples from all partitions
`count_genome_cuts()`	Counts DNase-seq or ATAC-seq cuts along the genome
`count_normalize_chip()`	Counts and normalizes (and transforms) ChIP-seq read coverage
`extract_TOP_coef_samples()`	Extracts regression coefficients from TOP posterior samples
`extract_TOP_mean_coef()`	Extracts the posterior mean of regression coefficients for each level of TOP model
`extract_tf_cell_combos()`	Creates a table listing the indices and names of TF and cell type combinations from the assembled training data
`fimo_motif_matches()`	Runs `FIMO` to scan for motif matches
`fit_TOP_M5_model()`	Fits TOP model with M5 bins
`get_sites_counts()`	Extracts count matrices around candidate binding sites
`get_total_reads()`	Gets total number of mapped reads from the `idxstats` file
`index_fa()`	Indexes the FASTA file, and generates a ‘chrom.sizes’ file
`merge_normalize_bin_transform_counts()`	Merges DNase or ATAC-seq counts from multiple replicates, then normalizes, bin and transform the merged counts
`merge_normalize_counts()`	Merges DNase or ATAC-seq counts from multiple replicates, then normalizes merged counts.
`millipede_binning()`	Performs `MILLIPEDE` binning on count matrix
`normalize_bin_transform_counts()`	Normalizes, bins and transforms counts
`normalize_chip()`	Normalizes (and transforms) ChIP-seq read coverage
`normalize_counts()`	Normalizes read counts
`plot_profile()`	Plots DNase or ATAC profiles
`plot_profile_strands()`	Plots DNase or ATAC profiles by strands of motif matches
`predict_TOP()`	Predicts quantitative TF occupancy or TF binding probability
`process_candidate_sites()`	Obtains and filters candidate sites from FIMO result
`scatterplot_predictions()`	Scatter plot of measured and predicted occupancy
`sort_index_idxstats_bam()`	Sorts, indexes the BAM file, and retrieves the `idxstats`.

Reference

All functions