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DESCRIPTION
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Package: bamSliceR
Type: Package
Title: Slicing and Tallied BAMs from GDC and local for Variants Analysis
Version: 0.99.3
Authors@R: c(
person("Peter", "Huang", role=c("aut", "cre"),
email="[email protected]",
comment=c(ORCID="0009-0004-5689-0193")),
person("Lauren", "Harmon", role=c("ctb"),
email="[email protected]",
comment=c(ORCID="0000-0002-2248-060")),
person("Timothy", "Triche", role=c("ctb"),
comment=c(ORCID="0000-0001-5665-946X")))
Description: A standardized pipeline for extracting, annotating, and analyzing genomic variants across large controlled-access repositories.
Depends: R (> 4.0),
gmapR,
VariantAnnotation,
GenomicRanges,
plyranges,
GenomicDataCommons,
Rsamtools,
rtracklayer
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
VignetteBuilder: knitr
biocViews: DataImport, Sequencing
Suggests:
knitr,
rmarkdown,
pkgdown
Imports:
BiocParallel,
biomaRt,
Homo.sapiens,
httr,
jsonlite,
stringr,
BSgenome.Hsapiens.UCSC.hg38,
TxDb.Hsapiens.UCSC.hg38.knownGene,
VariantTools,
data.table,
maftools,
RColorBrewer,
IRanges,
S4Vectors,
methods