bioc-issue-bot
commented
5 years ago Hi @bioinformatist
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: CrossICC
Type: Package
Title: An Iteractive Consensus Clustering Framework for Multi-platform Data Analysis
Version: 0.1.0
Description: Unsupervised clustering of high-throughput molecular profiling data is widely adopted for discovering cancer subtypes. However, cancer subtypes derived from a single dataset are not usually applicable across multiple datasets from different platforms. We previously published an iterative clustering algorithm to address the issue (see this paper), but its use was hampered due to lack of implementation. In this work, we presented CrossICC that was an R package implementation of this method. Moreover, many new features were added to improve the performance of the algorithm. Briefly, CrossICC utilizes an iterative strategy to derive the optimal gene set and cluster number from consensus similarity matrix generated by consensus clustering. CrossICC is able to deal with multiple cross platform datasets so that requires no between-dataset normalizations. This package also provides abundant functions to help users visualize the identified subtypes and evaluate the subtyping performance. Specially, many cancer-related analysis methods are embedded to facilitate the clinical translation of the identified cancer subtypes.
Authors@R: as.person(c(
"Yu Sun <sun_yu@mail.nankai.edu.cn> [aut, cre]",
"Qi Zhao <zhaoqi@sysucc.org.cn> [aut]"
))
License: file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: rmarkdown, testthat, knitr
RoxygenNote: 6.1.1
Imports: data.table,
methods,
ConsensusClusterPlus,
limma,
MergeMaid,
cluster,
pheatmap,
shiny,
RColorBrewer,
ggplot2,
shinydashboard,
shinyWidgets,
shinycssloaders,
DT,
ggthemes,
dplyr,
tibble
Depends: R (>= 2.10),
MASS,
Biobase
biocViews: Software
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
mtmorgan
bioinformatist
Liubuntu
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