Man pages for Maxim-Ivanov/TranscriptomeReconstructoR
Data-driven Annotation of the Transcriptome
| adjust_exons_of_long_reads | Adjust internal exons of full-length RNA-seq reads by... |
| call_TCs | Call TSS or PAS sites as clusters of reads from 5'- or 3'-tag... |
| call_transcribed_intervals | Call continuous intervals of nascent transcription from... |
| call_transcripts_and_genes | Call transcript and gene models from corrected full-length... |
| detect_alignment_errors | Detect the most common type of alignment errors in... |
| extend_long_reads_to_TSS_and_PAS | Adjust outer borders of full-length RNA-seq reads to the... |
| flip_strand_info | Flip strand orientation of a GenomicRanges object |
| load_BAM_files | Batch load BAM files |
| merge_GRanges | Merge coverage of GRanges objects |
| process_nascent_intervals | Classify intervals of nascent transcription and add them to... |
| refine_transcripts_by_annotation | Refine called transcripts by an existing transcript model |
| save_GRanges_as_bedGraph | Save stranded GRanges object as bedGraph file with strand... |
| write_grl_as_bed12 | Save GRangesList object as BED12 file |
