API for yasin-uzun/SINBAD.0.2
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_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
filter_cell Source code
filter_mapq Source code
filter_non_conversion 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
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
process_with_Seurat 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
split_lambda_old Source code
test Source code
trim_fastq_files 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_annots Source code
wrap_trim_fastq_files Source code
wrap_trim_stats Source code
yasin-uzun/SINBAD.0.2 documentation built on Dec. 23, 2021, 7:16 p.m.