Man pages for tanaylab/misha.ext
A home to functions that extend the misha package
| convert_10x_peak_names_to_misha_intervals | Convert 10X-format peak names to misha intervals |
| convert_misha_intervals_to_10x_peak_names | Convert misha intervals to 10X-format peak names |
| fwrite_header | writes a data frame with a header |
| fwrite_igv | Write IGV file from intervals set data frame |
| fwrite_ucsc | Write USCS genome browser file from intervals set data frame |
| gcluster.run2 | Runs R commands on a cluster that supports SGE |
| genome_exists | Does a genome db exist at the config file |
| get_promoters | Define promoter regions |
| gextract.left_join | Returns the result of track expressions evaluation for each... |
| gextract_meth | gextract methylation data |
| gintervals.align | Align intervals to the closest intervals in another set |
| gintervals.centers | Calculate the centers of intervals set |
| gintervals.distance | Calculate pairwise distance between interval sets |
| gintervals.expand | Exapnd an intervals set |
| gintervals.filter | Filter intervals set by distance to another. A wrapper around... |
| gintervals.mark_overlaps | Mark overlapping intervals with a group ID |
| gintervals.neighbors1 | Finds neighbors between two sets of intervals (and does not... |
| gintervals.normalize | Normalize an intervals set to be of the same length |
| gintervals.remove_overlaps | Remove overlapping intervals by selecting one interval per... |
| grandom_genome | Generate random genome intervals |
| gseq.create_track | Create sequence tracks for misha database |
| gset_genome | Set misha root based on genome name |
| gtrack.import_mappedseq_bam | Wrapper around gtrack.import_mappedseq for (multiple) bam... |
| gtrack.marginal_sum | Create a dense track that is a sum of misha tracks |
| gvtrack.array_extract | Extract a virtual track on each array.track column |
| intervs_to_mat | Transform an intervals set to matrix |
| mat_to_intervs | Transform a matrix with coordinate rownames to intervals set |
| misha.ext-package | misha.ext: A home to functions that extend the misha package |
| null-default | Default value for 'NULL'. |
| pipe | Pipe operator |
| reexports | Objects exported from other packages |
