Man pages for neurogenomics/PeakyFinders
Mining, Calling, and Importing Epigenomic Peaks in R
| bam_to | Convert a BAM file |
| bed_to | Convert a BED file |
| call_peaks | Call peaks |
| call_peaks_macsr | Call peaks: MACSr |
| call_peaks_seacr | Call peaks: SEACR |
| clean_granges | Clean GenomicRanges |
| condense_granges | Condense GRanges |
| construct_searches | Construct searches |
| create_trackhub | Create TrackHub |
| dt_to_granges | Convert data.table to GRanges object |
| example_bam | Example BAM files |
| example_bg_bw | Example bedGraph/bigWig files |
| filter_chrom | Filter chromosomes |
| find_executable_seacr | Find executable: 'SEACR' |
| find_links | Find links |
| fix_seqinfo | Fix bigWig |
| get_encode_peaks_metadata | Get ENCODE peaks metadata |
| get_genome | Get genome |
| get_geo_links | Get GEO supplementary files. |
| get_geo_supplementary_files | Get GEO supplementary files. |
| import_bedgraph_chroms | Get chromosomes |
| import_bigwig_filtered | Import filtered bigwig |
| import_peaks | Import peaks |
| import_peaks_annotationhub | Import peaks: AnnotationHub |
| import_peaks_encode | Import peaks: ENCODE |
| import_peaks_files | Import peaks: files |
| import_peaks_geo | Import peaks: GEO |
| import_peaks_multi | Import peaks: multi |
| import_peaks_roadmap | Import peaks: ROADMAP |
| is_granges | Is an object of class GRanges |
| is_local | Is local |
| is_url | Check if the input is url e.g. http:// or ftp:// |
| liftover_grlist | Liftover peak list |
| make_conda_env | Make conda environment |
| merge_bam | Merge BAM files |
| message_parallel | Message parallel |
| messager | Print messages |
| peaks_metadata_annotationhub | Metadata for epigenomic peaks: AnnotationHub |
| peaks_metadata_encode | Get ENCODE peaks metadata |
| peaks_metadata_roadmap | Metadata for epigenomic peaks: ROADMAP |
| pooled_peaks | Pooled peaks |
| pooled_peaks_macsr | Call consensus peaks: 'MACSr' |
| pooled_peaks_seacr | Call consensus peaks: 'SEACR' |
| report_time | Report time |
| search_annotationhub | Search metadata: AnnotationHub |
| search_encode | Search metadata: ENCODE |
| search_roadmap | Search metadata: ENCODE |
| stopper | Stop messages |
| translate_genome | Translate genome |
| unlist_dt | Unlist a data.table |
| unnest_wider_dt | Unnest data.table wider |
