API for yasin-uzun/SINBAD
A Single Cell DNA Methylation Data Processing Pipeline
| Global functions | |
|---|---|
| add_feature_to_Seurat_object | Source code |
| align_cell | Source code |
| align_sample | Source code |
| call_methylation_sites_for_cell | Source code |
| call_methylation_sites_for_sample | Source code |
| choose.dir | Source code |
| compute_aggr_met_rate | Source code |
| compute_call_count_matrices | Source code |
| compute_clusters | 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 |
| ensure_annot_list | Source code |
| file.choose | Source code |
| filter_cell | Source code |
| filter_mapq | Source code |
| filter_non_conversion | Source code |
| find_failed_alignments | Source code |
| find_failed_met_calls | Source code |
| generate_Seurat_object | Source code |
| get_divergent_color_set | Source code |
| get_fast_files | Source code |
| get_marker_genes | Source code |
| get_met_call_counts | Source code |
| get_promoters | Source code |
| get_r2_indeces_from_r1 | Source code |
| impute_nas | Source code |
| intersect_bed | Source code |
| merge_r1_and_r2_alignment_stats | Source code |
| merge_r1_and_r2_bam_for_cell | Source code |
| merge_r1_and_r2_bam_for_sample | Source code |
| plot_alignment_stats | Source code |
| plot_dim_red | Source code |
| plot_feature | Source code |
| plot_features | Source code |
| plot_preprocessing_results | Source code |
| plot_site_counts | 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 |
| render_image | 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 |
| server | Source code |
| split_lambda | Source code |
| split_lambda_old | Source code |
| test | Source code |
| trim_fastq_files | Source code |
| try_create_object | Source code |
| wrap_align_sample | Source code |
| wrap_call_methylation_sites | Source code |
| wrap_compute_coverage_rates | Source code |
| wrap_demux_fastq_files | Source code |
| wrap_demux_stats | 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_impute_nas | Source code |
| wrap_merge_r1_and_r2_bam | Source code |
| wrap_plot_alignment_stats | Source code |
| wrap_plot_features | Source code |
| wrap_plot_met_stats | Source code |
| wrap_plot_preprocessing_stats | Source code |
| wrap_quantify_regions | Source code |
| wrap_read_annot | Source code |
| wrap_remove_temporary_files | Source code |
| wrap_trim_fastq_files | Source code |
| wrap_trim_stats | Source code |
