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 |