Package: SCANVIS 1.19.0

Phaedra Agius

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

SCANVIS is a set of annotation-dependent tools for analyzing splice junctions and their read support as predetermined by an alignment tool of choice (for example, STAR aligner). SCANVIS assesses each junction's relative read support (RRS) by relating to the context of local split reads aligning to annotated transcripts. SCANVIS also annotates each splice junction by indicating whether the junction is supported by annotation or not, and if not, what type of junction it is (e.g. exon skipping, alternative 5' or 3' events, Novel Exons). Unannotated junctions are also futher annotated by indicating whether it induces a frame shift or not. SCANVIS includes a visualization function to generate static sashimi-style plots depicting relative read support and number of split reads using arc thickness and arc heights, making it easy for users to spot well-supported junctions. These plots also clearly delineate unannotated junctions from annotated ones using designated color schemes, and users can also highlight splice junctions of choice. Variants and/or a read profile are also incoroporated into the plot if the user supplies variants in bed format and/or the BAM file. One further feature of the visualization function is that users can submit multiple samples of a certain disease or cohort to generate a single plot - this occurs via a "merge" function wherein junction details over multiple samples are merged to generate a single sashimi plot, which is useful when contrasting cohorots (eg. disease vs control).

Authors:Phaedra Agius <[email protected]>

SCANVIS_1.19.0.tar.gz
SCANVIS_1.19.0.zip(r-4.5)SCANVIS_1.19.0.zip(r-4.4)SCANVIS_1.19.0.zip(r-4.3)
SCANVIS_1.19.0.tgz(r-4.4-any)SCANVIS_1.19.0.tgz(r-4.3-any)
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SCANVIS.pdf |SCANVIS.html✨
SCANVIS/json (API)

# Install 'SCANVIS' in R:
install.packages('SCANVIS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • GBM - List of 3 TCGA glioblastoma samples, parts thereof, outputs of SCANVISscan and SCANVISlinkvar functions with toy variants supplied for the variant-SJ mapping
  • 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
  • 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

On BioConductor:SCANVIS-1.19.0(bioc 3.20)SCANVIS-1.18.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

9 exports 0.49 score 50 dependencies

Last updated 2 months agofrom:f8a646fde7

Exports:gene2roiIR2Matls_urlSCANVISannotationSCANVISlinkvarSCANVISmergeSCANVISread_STARSCANVISscanSCANVISvisual

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslplotrixR6RCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc

SCANVIS

Rendered fromrunningSCANVIS.Rnwusingknitr::knitron Jun 30 2024.

Last update: 2019-06-24
Started: 2019-04-22