bioc-issue-bot
commented
3 years ago Hi @jackieduckie
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: svaRetro
Type: Package
Title: Retrotransposed transcript detection from structural variants
Version: 0.99.8
Date: 2021-04-15
Authors@R: c(
person("Ruining", "Dong", email="lnyidrn@gmail.com", role=c("aut","cre"), comment=c(ORCID = "0000-0003-1433-0484")))
Description: svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls.
It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites.
The candidate RTs are reported by events and annotated with information of the inserted transcripts.
License: GPL-3
Depends:
GenomicRanges,
rtracklayer,
VariantAnnotation,
StructuralVariantAnnotation,
BiocGenerics,
R (>= 4.1)
Imports:
assertthat,
Biostrings,
stringr,
dplyr,
methods,
rlang,
GenomicFeatures,
GenomeInfoDb,
utils
Suggests:
BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene,
ggplot2,
devtools,
testthat (>= 2.1.0),
roxygen2,
knitr,
plyranges,
circlize,
tictoc,
IRanges,
S4Vectors,
stats,
SummarizedExperiment
RoxygenNote: 7.1.1
Encoding: UTF-8
VignetteBuilder: knitr
biocViews: DataImport, Sequencing, Annotation, Genetics, VariantAnnotation, Coverage, VariantDetection
BugReports: https://github.com/PapenfussLab/svaRetro/issues
jackieduckie
nturaga
lshep
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