API for yasin-uzun/SINBAD.0.1
A Single Cell DNA Methylation Data Processing Pipeline
| Global functions | |
|---|---|
| align_cell | Source code |
| align_sample | Source code |
| call_methylation_sites_for_cell | Source code |
| call_methylation_sites_for_sample | Source code |
| compute_coverage_rates | Source code |
| compute_pca | Source code |
| compute_region_met_matrix | Source code |
| compute_umap | Source code |
| construct_sinbad_object | Source code |
| convert_to_granges | Source code |
| count_bam_files | Source code |
| count_fastq_reads | Source code |
| demux_fastq_files | Source code |
| dens_clus | Source code |
| dm_stat_test | Source code |
| dm_stat_test_for_clusters | Source code |
| filter_mapq | Source code |
| filter_non_conversion | Source code |
| get_divergent_color_set | Source code |
| get_marker_genes | Source code |
| get_promoters | Source code |
| intersect_bed | Source code |
| plot_alignment_stats | Source code |
| plot_dim_red | Source code |
| plot_feature | Source code |
| plot_preprocessing_results | Source code |
| plot_split_reports | Source code |
| process_bismark_alignment_reports | Source code |
| process_bismark_bias_report | Source code |
| process_bismark_bias_reports | Source code |
| process_bismark_split_reports | Source code |
| process_cutadapt_logs | Source code |
| process_sample_wrapper | Source code |
| read_configs | Source code |
| read_demux_logs | Source code |
| read_region_annot | Source code |
| reduce_dims_for_sample | Source code |
| remove_duplicate_reads | Source code |
| replace_nas_by_column_mean | Source code |
| replace_nas_by_row_mean | Source code |
| run_bismark_aligner | Source code |
| run_bs_seeker_aligner | Source code |
| run_bsmap_aligner | Source code |
| split_lambda | Source code |
| test | Source code |
| trim_fastq_files | Source code |
| wrap_align_sample | Source code |
| wrap_call_methylation_sites | Source code |
| wrap_demux_fastq_files | Source code |
| wrap_dim_red | Source code |
| wrap_dmr_analysis | Source code |
| wrap_generate_alignment_stats | Source code |
| wrap_generate_methylation_stats | Source code |
| wrap_quantify_regions | Source code |
| wrap_read_regions | Source code |
| wrap_trim_fastq_files | Source code |
