Man pages for AllenInstitute/lowcat
Low Coverage Accessibility and Transcriptomics
| all_column_correlation | Compare matrices and return a matrix with the correlations of... |
| balance_fragment_clusters | Downsample fragments within cluster sets to match the sample... |
| bam_to_fragment_list | Read multiple paired-end BAM files as a list of GRanges... |
| bed_to_GRanges | Convert data.frames in BED-like format to GRanges objects |
| bed_to_ucsc_loc | Convert GenomicRanges objects to a vector of UCSC browser... |
| build_pile_heatmap | Build a multi-track pileup heatmap |
| build_pile_plot | Build a multi-track pileup plot |
| cat_update | cat for replaceable messages |
| clusterApplyLB_chunks | Run clusterApplyLB across a single variable, N, using chunks... |
| collapse_fragment_list | Collapse a list of GenomicRanges objects to a single, merged... |
| combine_group_GRanges | Combine individual GRanges from a list of GRanges objects... |
| compare_fragment_lists | Compare two lists of GRanges to get counts or overlap... |
| convert_fragment_list | Convert a list of fragments to cut sites or Tn5 footprints |
| count_fragment_overlaps | Count the number of times a list of GenomicRanges objects... |
| downsample_fragments | Equally downsample a list of GenomicRanges objects |
| expand_fragments | Expand the boundaries of regions in a list of GenomicRanges... |
| filter_fragments | Filter a list of GenomicRanges objects against a single... |
| fragments_to_windows | Convert a list of GenomicRanges objects to a list of genomic... |
| get_gene_bodies | Read gene body locations from the UCSC RefGenes table |
| get_great_regions | Generate regions similar to GREAT based on the UCSC RefGenes... |
| get_tss_regions | Read TSS regions from the UCSC RefGenes table |
| GRanges_to_bed | Convert UCSC-style genomic locations to a BED-like data.frame |
| GRanges_to_ucsc_loc | Convert GenomicRanges objects to a vector of UCSC browser... |
| hello | Hello, World! |
| matrix_var_filter | Filter a matrix based on standard deviation of variance |
| max_column_correlation | Compare matrices to find the maximum correlation of columns |
| merge_bam_files | Merge multiple BAM files to a single output BAM file |
| overlap_jaccard_df | Compute jaccard similarity values based on GenomicRanges... |
| overlap_jaccard_df_fun | Linking function for computing jaccard similarity scores... |
| overlap_jaccard_mat | Compute jaccard similarity values based on GenomicRanges... |
| overlap_jaccard_mat_fun | Linking function for computing jaccard similarity scores... |
| percent_display | Convert i and n_chunks into a percentage character object. |
| pe_to_frag | Read a paired-end BAM file as GRanges fragments |
| pe_to_frag_parallel | Linking function for running pe_to_frag in parallel mode. |
| pileup_gr_list | Pileup reads, fragments, or cuts from a BAM file over target... |
| read_multiplexed_paired_bam | Read a multiplexed, paired-end BAM file and convert to a... |
| region_fragment_count | Count the sum of overlaps for each member of a fragment list... |
| res_to_distance_matrix | Convert jaccard similarity results from data.frame-based... |
| run_fragment_overlap_jaccard_parallel | For compatibility with older scripts |
| run_fragment_overlap_jaccard_parallel_full | For compatibility with older scripts |
| run_pe_to_frag_parallel | Read paired-end BAM files to GenomicRanges objects in... |
| run_se_to_cuts_parallel | Read single-end BAM files to GenomicRanges objects in... |
| run_window_overlap_jaccard_parallel | For compatibility with older scripts |
| se_to_cuts | Read a single-end BAM file as GRanges cut sites based on the... |
| se_to_cuts_parallel | Linking function for running se_to_cuts in parallel mode. |
| time_display | Display time elapsed and projected completion time. |
| ucsc_loc_to_bed | Convert GenomicRanges to a bed-like data.frame |
| ucsc_loc_to_GRanges | Convert UCSC-style genomic locations to a GenomicRegions... |
| window_jaccard_df | Compute jaccard similarity values based on window overlaps in... |
| window_jaccard_df_fun | Linking function for computing jaccard similarity scores... |
