Man pages for HarteminkLab/TOP
Predict transcription factor occupancy using DNase- or ATAC-seq data
| 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... |
| bin_transform_counts | Bins and transforms count matrix |
| combine_TOP_samples | Combines and takes the average of TOP posterior samples from... |
| 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_tf_cell_combos | Creates a table listing the indices and names of TF and cell... |
| extract_TOP_coef_samples | Extracts regression coefficients from TOP posterior samples |
| extract_TOP_mean_coef | Extracts the posterior mean of regression coefficients for... |
| 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,... |
| merge_normalize_counts | Merges DNase or ATAC-seq counts from multiple replicates,... |
| 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'. |
