Man pages for TearsWillFall/tfProfiling
An implementation of PeterUlz (https://github.com/PeterUlz/TranscriptionFactorProfiling) TranscriptionFactorProfiling pipeline in R for GNU/Unix based systems
| accessibility_score | Estimates the unranked Accesibility score for TFBS |
| analyze_tfbs_around_position | Analyze Mean Coverage Depth around TFBS |
| analyze_tfs | Analyze TFs for a sample |
| calculate_coverage_around_gp | Calculate Mean Coverage Depth around Genomic Position |
| calculate_coverage_tfbs | Calculate Mean Coverage Depth around TFBS |
| calculate_genowide_coverage | Calculate Genome-wide coverage for a BAM file |
| char2seed | Generate seed from non-symbolic characters |
| find_peaks | Calls maximum and minimum peaks |
| get_coverage_bed | Get coverage for target regions |
| get_high_signal | Filters high signal frequency in TFBS coverage data |
| get_low_signal | Filters low signal frequency in TFBS coverage data |
| get_mean_and_conf_intervals | Calculate mean and confidence intervals for positions... |
| get_mean_coverage | Calculate mean genome coverage |
| get_norm_local_coverage | Get normalized local coverage from segmentation data (CNA)... |
| install_required_tools | Installs all the required tools for the analysis. |
| pipe | Pipe operator |
| plot_freq_decomposition | Plot frequency decomposition for TFBS coverage data |
| plot_motif_coverage | Plot Mean Depth Coverage for TFBS |
| rank_accessibility | Ranks the Accessibility Score for all the TFs |
