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DESCRIPTION
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DESCRIPTION
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Package: jcc
Type: Package
Title: Calculate JCC Scores
Version: 0.1.0
Author: Charlotte Soneson and Michael I Love
Maintainer: Charlotte Soneson <charlottesoneson@gmail.com>
Description: The JCC scores are aimed at detecting genes for which estimated
transcript abundances are unreliable, either because of problems in the
transcript abundance estimation or because of missing or wrongly annotated
reference transcripts. It does so by comparing the number of reads
predicted to align across each junction, inferred from the transcript
abundances and a fragment bias model, to the observed number of
junction-spanning reads, obtained via alignment of the reads to the genome.
A high JCC score for a gene indicates that the estimated abundances for
the corresponding transcripts are unreliable and should be treated with
care in downstream analyses.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5)
Imports: GenomicFeatures,
ensembldb,
S4Vectors,
GenomeInfoDb,
Rsamtools,
GenomicRanges,
dplyr,
alpine,
stats,
parallel,
Gviz,
scatterpie (>= 0.1.2),
cowplot,
ggplot2 (>= 3.0.0),
rtracklayer,
grDevices,
IRanges
RoxygenNote: 7.3.0
Suggests: knitr,
rmarkdown,
BiocStyle,
BSgenome.Hsapiens.NCBI.GRCh38,
testthat
VignetteBuilder: knitr
biocViews: RNASeq, Coverage, Transcriptomics