API for HarteminkLab/TOP
Predict transcription factor occupancy using DNase- or ATAC-seq data
| Global functions | |
|---|---|
| add_chip_peak_labels_to_sites | Man page Source code |
| add_chip_signals_to_sites | Man page Source code |
| assemble_partition_training_data | Source code |
| assemble_training_data | Man page Source code |
| bedGraphToBigWig | Source code |
| bin_transform_counts | Man page Source code |
| combine_TOP_samples | Man page Source code |
| count_genome_cuts | Man page Source code |
| count_genome_cuts_nobedtools | Source code |
| count_normalize_chip | Man page Source code |
| extract_TOP_coef_samples | Man page Source code |
| extract_TOP_mean_coef | Man page Source code |
| extract_tf_cell_combos | Man page Source code |
| filter_blacklist | Source code |
| filter_mapability | Source code |
| fimo_motif_matches | Man page Source code |
| fit_TOP_M5_model | Man page Source code |
| fit_TOP_logistic_M5_model_jags | Source code |
| fit_TOP_occupancy_M5_model_jags | Source code |
| flank_fimo_sites | Source code |
| flip_neg_strand_counts | Source code |
| get_sites_counts | Man page Source code |
| get_total_reads | Man page Source code |
| index_fa | Man page Source code |
| merge_normalize_bin_transform_counts | Man page Source code |
| merge_normalize_counts | Man page Source code |
| millipede_binning | Man page Source code |
| normalize_bin_transform_counts | Man page Source code |
| normalize_chip | Man page Source code |
| normalize_counts | Man page Source code |
| plot_profile | Man page Source code |
| plot_profile_strands | Man page Source code |
| predict_TOP | Man page Source code |
| predict_TOP_logistic_mean_coef | Source code |
| predict_TOP_mean_coef | Source code |
| predict_TOP_samples | Source code |
| process_candidate_sites | Man page Source code |
| read_bam_cuts | Source code |
| read_bam_cuts_ATACreadpairs | Source code |
| scatterplot_predictions | Man page Source code |
| select_TOP_samples | Source code |
| select_features | Source code |
| select_model_coef_level | Source code |
| sort_index_idxstats_bam | Man page Source code |
