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| SCANVIS-package | SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions |
| GBM | list of 3 TCGA glioblastoma samples, parts thereof, outputs of SCANVISscan and SCANVISlinkvar functions with toy variants supplied for the variant-SJ mapping |
| gbm3 | part of a TCGA glioblastoma sample from STAR alignment SJ.tab file |
| gbm3.vcf | a toy set of 6 variants that pair up with the gbm3 data example |
| gen19 | parts of the annotation object created by the SCANVISannotation function when used with the url ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/ which references the gencode v19 GTF file for human hg19 |
| gene2roi | gene name/s to region of interest |
| IR2Mat | IRanges to Matrix |
| ls_url | list files available at annotation/gencode url |
| LUAD | list of 3 TCGA lung adenocarcinoma samples, parts thereof, outputs of SCANVISscan |
| LUSC | list of 3 TCGA lung squamous cell carcinoma samples, parts thereof, both outputs of SCANVISscan with the second sample being variant-mapped via SCANVISlinkvar |
| SCANVIS | SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions |
| SCANVISannotation | assembles annotation from gtf file into SCANVISreadable format |
| SCANVISexamples | Data for running SCANVISexamples |
| SCANVISlinkvar | maps variants to SCANVISscored junctions |
| SCANVISmerge | merges multiple SCANVISsamples |
| SCANVISread_STAR | upload SJ.tab STAR file in SCANVISuse |
| SCANVISscan | SCore and ANnotate splice junctions |
| SCANVISvisual | a sashimi-style visualization tool |