Man pages for neurogenomics/EpiCompare
Comparison, Benchmarking & QC of Epigenomic Datasets
| as_interactive | As interactive |
| bpplapply | Wrapper for bplapply |
| checkCache | Check cache |
| check_cell_lines | Check cell lines |
| check_genome_build | Check genome build |
| check_grlist_cols | Check GRanges list columns |
| check_list_names | Check peaklist is named |
| check_workers | Check workers |
| clean_granges | Clean GRanges |
| CnR_H3K27ac | Example CUT&Run peak file |
| CnR_H3K27ac_picard | Example Picard duplication metrics file 2 |
| CnT_H3K27ac | Example CUT&Tag peak file |
| CnT_H3K27ac_picard | Example Picard duplication metrics file 1 |
| compute_consensus_peaks | Compute consensus peaks |
| compute_corr | Compute correlation matrix |
| download_button | Download local file |
| encode_H3K27ac | Example ChIP-seq peak file |
| EpiCompare | Compare epigenomic datasets |
| fig_length | Dynamic Figure Length Generator |
| fragment_info | Summary on fragments |
| gather_files | Gather files |
| gather_files_names | Make file names |
| get_bpparam | Get BiocParallel parameters |
| get_chromHMM_annotation | Download ChromHMM annotation file(s) |
| group_files | Group files |
| hg19_blacklist | Human genome hg19 blacklisted regions |
| hg38_blacklist | Human genome hg38 blacklisted regions |
| is_granges | Is an object of class GRanges |
| liftover_grlist | Liftover peak list |
| message_parallel | Message parallel |
| messager | Print messages |
| mm10_blacklist | Mouse genome mm10 blacklisted regions |
| mm9_blacklist | Mouse genome mm9 blacklisted regions |
| overlap_heatmap | Generate heatmap of percentage overlap |
| overlap_percent | Calculate percentage of overlapping peaks |
| overlap_stat_plot | Statistical significance of overlapping peaks |
| overlap_upset_plot | Generate Upset plot for overlapping peaks |
| peak_info | Summary of Peak Information |
| plot_ChIPseeker_annotation | Create ChIPseeker annotation plot |
| plot_chromHMM | Plot ChromHMM heatmap |
| plot_corr | Plot correlation of peak files |
| plot_enrichment | Generate enrichment analysis plots |
| plot_precision_recall | Plot precision-recall curves |
| precision_recall | Compute precision-recall |
| precision_recall_matrix | Create a precision-recall matrix |
| predict_precision_recall | Predict precision-recall |
| predict_values | Predict values |
| prepare_blacklist | Prepare blacklist as GRanges |
| prepare_genome_builds | Prepare genome builds |
| prepare_peaklist | Prepare peaklist as GRanges |
| prepare_reference | Prepare referemce as GRanges |
| read_bowtie | Read bowtie |
| read_peaks | Read peaks |
| rebin_peaks | Rebin peaks |
| remove_nonstandard_chrom | Remove non-standard chromosomes |
| report_command | Report command |
| report_header | Report header |
| save_output | Save output |
| set_min_max | Set min/max |
| stopper | Stop messages |
| tidy_chromosomes | Remove odd chromosomes from GRanges objects |
| tidy_peakfile | Tidy peakfiles in GRanges |
| translate_genome | Translate genome |
| tss_plot | Read count frequency around TSS |
| width_boxplot | Peak width boxplot |
| write_example_peaks | Write example peaks |
