bioc-issue-bot
commented
2 years ago Hi @jeffreypullin
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:
Type: Package
Package: cardelino
Title: Clone Identification from Single Cell Data
Version: 0.99.0
Authors@R:
c(person(given = "Jeffrey",
family = "Pullin",
role = c("aut", "cre"),
email = "jpullin@svi.edu.au"),
person(given = "Yuanhua",
family = "Huang",
role = "aut",
email = "yuanhua@hku.hk"),
person(given = "Davis",
family = "McCarthy",
role = "aut",
email = "dmccarthy@svi.edu.au"))
Description: Methods to infer clonal tree configuration for a population of
cells using single-cell RNA-seq data (scRNA-seq), and possibly other data
modalities. Methods are also provided to assign cells to inferred clones
and explore differences in gene expression between clones. These methods
can flexibly integrate information from imperfect clonal trees inferred
based on bulk exome-seq data, and sparse variant alleles expressed in
scRNA-seq data. A flexible beta-binomial error model that accounts for
stochastic dropout events as well as systematic allelic imbalance is used.
License: GPL (>= 3)
URL: https://github.com/single-cell-genetics/cardelino
BugReports: https://github.com/single-cell-genetics/cardelino/issues
Depends:
R (>= 4.2),
stats
Imports:
GenomeInfoDb,
GenomicRanges,
ggplot2,
ggtree,
Matrix,
matrixStats,
methods,
pheatmap,
snpStats,
S4Vectors,
utils,
VariantAnnotation,
vcfR
Suggests:
BiocStyle,
combinat,
foreach,
knitr,
pcaMethods,
rmarkdown,
testthat,
VGAM
Enhances:
doMC
VignetteBuilder:
knitr
biocViews: SingleCell, RNASeq, Visualization, Transcriptomics,
GeneExpression, Sequencing, Software, ExomeSeq
Encoding: UTF-8
NeedsCompilation: yes
RoxygenNote: 7.2.0
vjcitn
ococrook
jeffreypullin
lshep
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