bioc-issue-bot
commented
3 years ago Hi @hui-sheen
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: MetaGSCA
Type: Package
Title: Meta-analysis of Gene Set differential Co-expression Analysis
Version: 0.99.0
Date: 2021-6-10
Authors@R: c(person("Yan", "Guo", role = c("aut"),
email = "yanguo1978@gmail.com"),
person("Fei", "Ye", role="aut", email = "fei.ye@vumc.org"),
person("Hui", "Yu", role=c("ctb", "cre"),
email = "schena.yu@gmail.com", comment=c(ORCID="0000-0002-4491-8855")))
Depends: R (>= 3.6.3), data.table, meta, grid, sjstats, igraph
Description: MetaGSCA systematically assesses the coexpression disturbance of a gene set by pooling the results from individual studies. A nonparametric approach named GSNCA (Rahmatallah 2014, Bioinformatics) is used to test whether the gene set is differentially co-expresssed between the two conditions, and a permutation test p-value is computed. Bootstrapping is used to construct confidence intervals of p-values. Meta-analysis is offered through two options: random-intercept logistic regression model and the inverse variance method. Lastly, a pathway crosstalk network is delineated based on the meta-analysis result outputted from the prior steps.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: false
biocViews: Software, DifferentialExpression, StatisticalMethod
RoxygenNote: 7.1.1
hui-sheen
lshep
hpages
Dear Bioconductor team,
Our R package MetaGSCA got published lately in PLoS Computational Biology (10.1371/journal.pcbi.1008976). Please note that we used to submit MetaGSCA to Bioconductor in last fall (issue #1568). Now the source code has been fundamentally re-written and thus significantly optimized. It has also been shifted under a different maintainer account. So this is a brand new submission, but I'm referring to the historical submission for your reference.
Thanks, Hui Yu ######################################################### Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
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