bioc-issue-bot
commented
3 years ago Hi @seriph78
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: COTAN
Type: Package
Title: COexpression Tables ANalysis
Version: 0.99.0
Authors@R: c(
person("Galfrè", "Silvia Giulia",email = "silvia.galfre@uniroma1.it", role=c("aut","cre"),comment = c(ORCID = "0000-0002-2770-0344")),
person("Morandin","Francesco", email = "francesco.morandin@unipr.it", role = "aut",comment = c(ORCID = "0000-0002-2022-2300")),
person("Pietrosanto","Marco", role = "aut",comment = c(ORCID = "0000-0001-5129-6065")),
person("Cremisi","Federico", role = "aut",comment = c(ORCID = "0000-0003-4925-2703")),
person("Helmer-Citterich","Manuela", role = "aut",comment = c(ORCID = "0000-0001-9530-7504")))
Description: Statistical and computational method to analyze the co-expression of
gene pairs at single cell level. It provides the foundation for single-cell gene
interactome analysis. The basic idea is studying the zero UMI counts’ distribution
instead of focusing on positive counts; this is done with a generalized contingency
tables framework. COTAN can effectively assess the correlated or anti-correlated
expression of gene pairs. It provides a numerical index related to the correlation and an
approximate p-value for the associated independence test. COTAN can also evaluate whether
single genes are differentially expressed, scoring them with a newly defined global
differentiation index. Moreover, this approach provides ways to plot and cluster genes
according to their co-expression pattern with other genes, effectively helping the study
of gene interactions and becoming a new tool to identify cell-identity marker genes.
URL: https://github.com/seriph78/COTAN
BugReports: https://github.com/seriph78/COTAN/issues
Depends: R (>= 4.1)
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.1.1
Imports:
dplyr,
methods,
grDevices,
Matrix,
ggplot2,
ggrepel,
stats,
parallel,
tibble,
tidyr,
basilisk,
reticulate,
ComplexHeatmap,
circlize,
grid,
scales,
utils,
rlang
Suggests:
testthat (>= 3.0.0),
spelling,
knitr,
data.table,
rmarkdown,
R.utils,
tidyverse,
htmlwidgets,
MASS,
factoextra,
Rtsne,
plotly,
dendextend,
cowplot
Config/testthat/edition: 3
SystemRequirements:
python
Language: en-US
biocViews:
SystemsBiology,
Transcriptomics,
GeneExpression,
SingleCell
VignetteBuilder: knitr
seriph78
nturaga
lshep
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