GBM                     list of 3 TCGA glioblastoma samples, parts
                        thereof, outputs of SCANVISscan and
                        SCANVISlinkvar functions with toy variants
                        supplied for the variant-SJ mapping
IR2Mat                  IRanges to Matrix
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-package         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
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
ls_url                  list files available at annotation/gencode url
