|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|
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