SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions


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Documentation for package ‘SCANVIS’ version 1.6.0

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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