API for hw538/cfDNAPro
cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA
| Global functions | |
|---|---|
| AllGroupMetrics | Source code |
| AllGroupMode_Dataframe | Source code |
| AllGroupMode_List | Source code |
| AllGroupPropCdfMeanMedian_Dataframe | Source code |
| AllGroupPropCdfMeanMedian_List | Source code |
| AllGroupPropCdfMean_Dataframe | Source code |
| AllGroupPropCdfMean_List | Source code |
| AllGroupPropCdfMedian_Dataframe | Source code |
| AllGroupPropCdfMedian_List | Source code |
| AllGroupPropCdf_Dataframe | Source code |
| AllGroupPropCdf_List | Source code |
| AllGroupPropMean_Dataframe | Source code |
| AllGroupPropMean_List | Source code |
| AllGroupPropMedian_Dataframe | Source code |
| AllGroupPropMedian_List | Source code |
| AllGroupProp_Dataframe | Source code |
| AllGroupProp_List | Source code |
| GroupPeakFocus | Source code |
| GroupValleyFocus | Source code |
| InsertSizeProp | Source code |
| InsertSizePropMean | Source code |
| InsertSizePropMedian | Source code |
| InsertSizePropMode | Source code |
| InterPeakDist | Source code |
| InterValleyDist | Source code |
| add_base_info | Source code |
| add_mutation_overlap_status | Source code |
| adjust_quality_for_deletions | Source code |
| adjust_ref_fragments | Source code |
| adjust_sequence_for_deletions | Source code |
| annotate_cnv_mut | Source code |
| apply_to_paired_reads | Source code |
| apply_to_paired_reads_ins | Source code |
| bam_count | Source code |
| bam_to_galp | Source code |
| bam_to_galp2 | Man page Source code |
| bam_to_galp_mut | Source code |
| calcualte_interpeak_dist | Source code |
| calcualte_intervalley_dist | Source code |
| calculate_breaks_for_mode_plot | Source code |
| calculate_labels_for_mode_plot | Source code |
| calculate_mean_for_df | Source code |
| calculate_mean_for_list | Source code |
| calculate_median_for_df | Source code |
| calculate_median_for_list | Source code |
| calculate_peaks | Source code |
| calculate_prop | Source code |
| calculate_prop_cdf | Source code |
| calculate_propcdf_mean_for_list | Source code |
| calculate_propcdf_meanmedian_for_list | Source code |
| calculate_propcdf_median_for_list | Source code |
| calculate_read_length | Source code |
| calculate_sample_max_prop | Source code |
| calculate_valleys | Source code |
| callCNV | Man page Source code |
| callLength | Man page Source code |
| callMetrics | Man page Source code |
| callMode | Man page Source code |
| callMotif | Man page Source code |
| callPeakDistance | Man page Source code |
| callSize | Man page Source code |
| callTrinucleotide | Man page Source code |
| callValleyDistance | Man page Source code |
| check_dup_mode | Source code |
| check_mutation_in_metadata | Source code |
| check_mutation_status | Source code |
| check_mutfile_columns | Source code |
| chr_count | Source code |
| clip_read_pair | Source code |
| create_empty_galp | Source code |
| curate_start_and_end | Source code |
| downsampleBam | Man page Source code |
| examplePath | Man page Source code |
| filter_insert_size | Source code |
| get_full_sample_name | Source code |
| get_genome_reference | Source code |
| get_group_path | Source code |
| get_highest_column | Source code |
| get_motif | Source code |
| get_trinucleotide | Source code |
| insertion_pos | Source code |
| integrate_motif_mut | Source code |
| loop_read_insert_metrics_in_list | Source code |
| make_granges | Source code |
| mm_del_pos | Source code |
| pileupMismatches | Man page Source code |
| plotAllToOne | Man page Source code |
| plotCNV | Man page Source code |
| plotLength | Man page Source code |
| plotMetrics | Man page Source code |
| plotMode | Man page Source code |
| plotModeSummary | Man page Source code |
| plotMotif | Man page Source code |
| plotPeakDistance | Man page Source code |
| plotSingleGroup | Man page Source code |
| plotTrinucData | Source code |
| plotTrinucleotide | Man page Source code |
| plotValleyDistance | Man page Source code |
| plot_length_mut | Source code |
| plot_motif_mut | Source code |
| prepare_data | Source code |
| processMotif | Man page Source code |
| processTrinucleotideData | Source code |
| process_bam_file | Source code |
| process_base_qualities | Source code |
| process_cnv_mut | Source code |
| process_columns | Source code |
| process_duplicate_read_pairs | Source code |
| process_insertions | Source code |
| process_length_mut | Source code |
| process_mutation_fragments | Source code |
| process_mutation_status | Source code |
| readBam | Man page Source code |
| readGALP | Man page Source code |
| read_bam_insert_metrics | Man page Source code |
| read_bam_insert_metrics_from_tlen | Source code |
| read_cfdnapro_insert_metrics | Source code |
| read_mutation_file | Source code |
| read_picard_insert_metrics | Source code |
| read_raw_data | Source code |
| remove_clustered_mutations | Source code |
| remove_insertion_bases | Source code |
| remove_insertion_qual_bases | Source code |
| remove_out_of_bound_reads | Source code |
| remove_outward_facing_readpairs | Source code |
| rleid_cfdnapro | Source code |
| select_and_normalize | Source code |
| stratify_mutation_status | Source code |
| summarizeBam | Man page Source code |
| summarize_fragment_lengths | Source code |
| summarize_mutational_data | Source code |
| theme_cnv_plot | Source code |
| theme_length_plot | Source code |
| theme_motif_plot | Source code Source code |
| theme_motif_plot_mut | Source code |
| update_consensus_mismatch | Source code |
| update_locus_status | Source code |
| update_mdi_columns | Source code |
| writeMutTable | Man page Source code |
