bioc-issue-bot
commented
5 months ago Hi @TomVuod
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: epiregulon
Title: Gene regulatory network inference from single cell epigenomic data
Version: 0.99.0
Date: 2023-11-21
Authors@R:
c(person(given = "Xiaosai", family = "Yao", role = c("aut", "cre"), email = "yao.xiaosai@gene.com", comment = c(ORCID = "0000-0001-9729-0726")),
person(given = "Tomasz", family = "Włodarczyk", role = c("aut"), email = "tomwlo@gmail.com", comment = c(ORCID = "0000-0003-1554-9699")),
person(given = "Aaron", family = "Lun", role=c("aut"), email="infinite.monkeys.with.keyboards@gmail.com"),
person(given = "Shang-Yang", family = "Chen", role = "aut", email = "sychen9584@gmail.com"))
Description: Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.
License: file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Imports:
BiocFileCache,
BiocParallel,
Matrix,
Rcpp,
S4Vectors,
SummarizedExperiment,
bluster,
checkmate,
entropy,
lifecycle,
methods,
scran,
scuttle,
stats,
utils,
scMultiome,
GenomeInfoDb,
GenomicRanges,
AUCell,
BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10,
motifmatchr
Depends:
R (>= 4.2.0),
SingleCellExperiment
Suggests:
knitr,
rmarkdown,
parallel,
BiocStyle,
testthat (>= 3.0.0),
coin,
scater
LinkingTo: Rcpp
VignetteBuilder: knitr
URL: https://github.com/xiaosaiyao/epiregulon/
biocViews: GeneExpression, Transcription, ChipOnChip, DifferentialExpression, GeneTarget, Normalization, GraphAndNetwork
Config/testthat/edition: 3
BugReports: https://github.com/xiaosaiyao/epiregulon/issues
vjcitn
xiaosaiyao
lshep
TomVuod
jianhong
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