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DESCRIPTION
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DESCRIPTION
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Package: Espresso
Title: Espresso - Somatic Mutation Calling using Contextual Error Models
Version: 0.0.0.9000
Authors@R: c(person("Andy", "Zeng", email = "andy.zeng@uhnresearch.ca", role = c("aut", "cre")), person("Sagi", "Abelson", email = "sagi.abelson@oicr.on.ca", role = c("aut", "ctb")), person("Ido", "Nofech-Mozes", email = "Ido.Nofech-Mozes@oicr.on.ca", role = c("ctb")))
Description: Traditional variant calling methods utilize variant allele frequency (VAF) cutoffs
to call variants. These cutoffs are often set arbitrarily and the measure becomes
problematic when trying to call at variants at low VAFs, where true biological variation
becomes hard to distinguish from sequencing error. The 'Espresso' package employs a novel
variant calling approach that models sequencing error distributions across 192 trinucleotide
contexts and conducts variant calling by comparing each putative variant to its corresponding
contextual error distribution. This demonstrates superior sensitivity and specificity over
existing variant calling methods and bolsters our ability to accurately distinguish signal
from noise at very low VAFs.
Depends: R (>= 3.5.0)
Imports: VariantAnnotation, doParallel, fitdistrplus, plyr, dplyr, stringr, data.table, rlang, foreach, Biostrings, GenomeInfoDb, methods, rtracklayer, GenomicRanges, S4Vectors, IRanges, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, GenomicScores, utils, vctrs, stats, BiocGenerics, maftools, cellbaseR
License: Apache License (== 2.0) | file LICENSE
Encoding: UTF-8
LazyData: true
Suggests:
knitr,
rmarkdown,
testthat
VignetteBuilder: knitr
RoxygenNote: 7.1.1