bioc-issue-bot
commented
1 year ago Hi @SONGDONGYUAN1994
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: scDesign3
Type: Package
Title: A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics
Version: 0.99.0
Authors@R:
c(person("Dongyuan", "Song", , "dongyuansong@ucla.edu", role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-1114-1215")),
person("Qingyang", "Wang", , "qw802@g.ucla.edu", role = c("aut"),
comment = c(ORCID = "0000-0002-1051-609X")))
Description: scDesign3 is an all-in-one statistical simulator to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real datasets. Furthermore, using a unified probabilistic model for single-cell and spatial omics data, scDesign3 can infer biologically meaningful parameters, assess the goodness-of-fit of cell clusters and trajectories, and generate in silico negative and positive controls for benchmarking computational tools.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Depends: R (>= 4.2.0)
Imports:
dplyr,
tibble,
stats,
methods,
mgcv,
gamlss,
gamlss.dist,
SummarizedExperiment,
SingleCellExperiment,
mclust,
Rfast,
mvtnorm,
parallel,
pbmcapply,
rvinecopulib,
umap,
ggplot2,
irlba,
viridis,
BiocParallel
Suggests:
magrittr,
Seurat,
Signac,
matrixcalc,
spcov,
knitr,
rmarkdown,
testthat (>= 3.0.0),
RefManageR,
dyngen,
cowplot,
ggraph,
ggrastr,
gridExtra,
reshape2,
scales,
spatialDE,
DESeq2,
DuoClustering2018,
NBAMSeq,
PseudotimeDE,
SPARK,
SeuratObject,
aricode,
ggh4x,
ggpubr,
ggrepel,
igraph,
monocle3,
scater,
scran,
stringr,
tidygraph,
tradeSeq,
useful,
sessioninfo,
gamlss.add,
BiocStyle,
tidyr,
tidyselect
biocViews:
Software,
SingleCell,
Sequencing,
GeneExpression,
Spatial
URL: https://github.com/SONGDONGYUAN1994/scDesign3
BugReports: https://github.com/SONGDONGYUAN1994/scDesign3/issues
RoxygenNote: 7.2.3
Config/testthat/edition: 3
VignetteBuilder: knitr
hpages
SONGDONGYUAN1994
lshep
JSB-UCLA
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