Package: NCutYX 0.1.1

NCutYX: Clustering of Omics Data of Multiple Types with a Multilayer Network Representation

Omics data come in different forms: gene expression, methylation, copy number, protein measurements and more. 'NCutYX' allows clustering of variables, of samples, and both variables and samples (biclustering), while incorporating the dependencies across multiple types of Omics data. (SJ Teran Hidalgo et al (2017), <doi:10.1186/s12864-017-3990-1>).

Authors:Sebastian J. Teran Hidalgo, Shuangge Ma, Ruofan Bie

NCutYX_0.1.1.tar.gz
NCutYX_0.1.1.zip(r-4.7)NCutYX_0.1.1.zip(r-4.6)NCutYX_0.1.1.zip(r-4.5)
NCutYX_0.1.1.tgz(r-4.6-x86_64)NCutYX_0.1.1.tgz(r-4.6-arm64)NCutYX_0.1.1.tgz(r-4.5-x86_64)NCutYX_0.1.1.tgz(r-4.5-arm64)
NCutYX_0.1.1.tar.gz(r-4.7-arm64)NCutYX_0.1.1.tar.gz(r-4.7-x86_64)NCutYX_0.1.1.tar.gz(r-4.6-arm64)NCutYX_0.1.1.tar.gz(r-4.6-x86_64)
NCutYX_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
NCutYX/json (API)

# Install 'NCutYX' in R:

install.packages('NCutYX', repos = c('https://seborinos.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/seborinos/ncutyx/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

brca.data.cna - Data on copy number aberrations from breast cancer patients.
brca.data.ge - Data on gene expression from breast cancer patients.
brca.data.rppa - Data on protein measurements from breast cancer patients.
cesc.data.cna - Data on copy number aberrations from cervical cancer patients.
cesc.data.ge - Data on gene expression from breast cancer patients.
cesc.data.rppa - Data on protein measurements from cervical cancer patients.

On CRAN:

c-plus-plus cancer-genomics clustering copy-number-variation devtools gene-expression graph-algorithms graph-cut graphs proteins rcpp cpp

4.48 score 4 stars 15 scripts 313 downloads 8 exports 18 dependencies

Last updated from:f245c58a2e. Checks:11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	WARNING	184
linux-devel-x86_64	WARNING	151
source / vignettes	OK	232
linux-release-arm64	WARNING	156
linux-release-x86_64	WARNING	152
macos-release-arm64	WARNING	168
macos-release-x86_64	WARNING	407
macos-oldrel-arm64	WARNING	208
macos-oldrel-x86_64	WARNING	255
windows-devel	WARNING	117
windows-release	WARNING	128
windows-oldrel	WARNING	139
wasm-release	OK	123

Exports:ancut awncut awncut.selection ErrorRate mlbncut muncut ncut pwncut

Dependencies:codetools dotCall64 fields foreach glmnet iterators lattice maps MASS Matrix mvtnorm RColorBrewer Rcpp RcppEigen shape spam survival viridisLite

The NCutYX package

Rendered frommy-vignette.Rmdusingknitr::rmarkdown

Last update: 2018-02-07
Started: 2018-02-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Cluster the Columns of Y into K Groups with the Help of External Features X.	ancut
Cluster the Rows of X into K Clusters Using the AWNCut Method.	awncut
This Function Outputs the Selection of Tuning Parameters for the AWNCut Method.	awncut.selection
Data on copy number aberrations from breast cancer patients.	brca.data.cna
Data on gene expression from breast cancer patients.	brca.data.ge
Data on protein measurements from breast cancer patients.	brca.data.rppa
Data on copy number aberrations from cervical cancer patients.	cesc.data.cna
Data on gene expression from breast cancer patients.	cesc.data.ge
Data on protein measurements from cervical cancer patients.	cesc.data.rppa
This Function Calculates the True Error Rate of a Clustering Result, Assuming that There are Three Clusters.	ErrorRate
The MLBNCut Clusters the Columns and the Rows Simultaneously of Data from 3 Different Sources.	mlbncut
MuNCut Clusters the Columns of Data from 3 Different Sources.	muncut
Cluster the Columns of Y into K Groups Using the NCut Graph Measure.	ncut
Cluster the Columns of X into K Clusters by Giving a Weighted Cluster Membership while shrinking Weights Towards Each Other.	pwncut