Man pages for asrinivasan-oa/gread
Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files
| as_bam | convert 'GAlignments' object to 'data.table' |
| as_data_table | Convert gtf/gff/bam/bed S4 objects to data.table and preserve... |
| as_granges | Convert data.table to GRanges object |
| bam-class | bam S4 class designed to store data of Binary sequence... |
| bed-class | bed S4 class designed to store data of Browser Extensible... |
| construct_introns | Construct introns from gtf/gff objects |
| disjoin_overlaps | Compute disjoint ranges on a gtf/gff/bed/bam object. |
| exon-class | exon S4 class designed to store exon data and dispatch to the... |
| extract | Extract features from gtf/gff objects |
| find_overlaps | Find overlapping indices of two gtf/gff/bed/bam objects |
| gene-class | gene S4 class designed to store gene data and dispatch to the... |
| gff-class | gff S4 class designed to store data of Gene Feature Format... |
| gread | Fast Reading and Processing of Common Gene Annotation and... |
| gtf-class | gtf S4 class designed to store data of Gene Transfer Format... |
| intersect_bed | Extract gtf coordinates intersecting input bed file |
| intersect_overlaps | Compute intersecting ranges on a gtf/gff/bed/bam object with... |
| intron-class | intron S4 class designed to store intron data and dispatch to... |
| non_overlaps | Generate non-overlapping intron coordinates |
| read_format | Quick and easy reading of gtf/gff/bed/bam files |
| reduce_overlaps | Compute reduced ranges on a gtf/gff/bed/bam object. |
| shallow | shallow copy a 'data.table' |
| strictly_nonunique | Return only those rows where rows per group is > 1. |
| supported_formats | Currently supported formats |
| test_gread | Run a set of tests |
