Package: GSBenchMark 1.33.0

Bahman Afsari

GSBenchMark: Gene Set Benchmark

Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al.

Authors:Bahman Afsari <[email protected]>, Elana J. Fertig <[email protected]>

GSBenchMark_1.33.0.tar.gz
GSBenchMark_1.33.0.tar.gz(r-4.7-any)GSBenchMark_1.33.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GSBenchMark/json (API)

# Install 'GSBenchMark' in R:

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

Datasets:

diracpathways - The pathways downloaded from DIRAC paper
exprsdata - Gene expression matrix from DIRAC paper
exprsdata - Gene expression matrix from DIRAC paper
exprsdata - Gene expression matrix from DIRAC paper
exprsdata - Gene expression matrix from DIRAC paper
exprsdata - Gene expression matrix from DIRAC paper
exprsdata - Gene expression matrix from DIRAC paper
exprsdata - Gene expression matrix from DIRAC paper
exprsdata - Gene expression matrix from DIRAC paper
exprsdata - Gene expression matrix from DIRAC paper
exprsdata - Gene expression matrix from DIRAC paper
exprsdata - Gene expression matrix from DIRAC paper
GSBenchMark.Dataset.names - The names of the datasets of gene expressions and phenotypes downloaded from DIRAC paper
logexprsdata - Gene expression matrix from DIRAC paper
logexprsdata - Gene expression matrix from DIRAC paper
logexprsdata - Gene expression matrix from DIRAC paper
logexprsdata - Gene expression matrix from DIRAC paper
logexprsdata - Gene expression matrix from DIRAC paper
logexprsdata - Gene expression matrix from DIRAC paper
logexprsdata - Gene expression matrix from DIRAC paper
logexprsdata - Gene expression matrix from DIRAC paper
logexprsdata - Gene expression matrix from DIRAC paper
logexprsdata - Gene expression matrix from DIRAC paper
logexprsdata - Gene expression matrix from DIRAC paper
phenotypes - A factor for binary phenotypes from DIRAC paper
phenotypes - A factor for binary phenotypes from DIRAC paper
phenotypes - A factor for binary phenotypes from DIRAC paper
phenotypes - A factor for binary phenotypes from DIRAC paper
phenotypes - A factor for binary phenotypes from DIRAC paper
phenotypes - A factor for binary phenotypes from DIRAC paper
phenotypes - A factor for binary phenotypes from DIRAC paper
phenotypes - A factor for binary phenotypes from DIRAC paper
phenotypes - A factor for binary phenotypes from DIRAC paper
phenotypes - A factor for binary phenotypes from DIRAC paper
phenotypes - A factor for binary phenotypes from DIRAC paper
phenotypesLevels - A factor for binary phenotypes from DIRAC paper
phenotypesLevels - A factor for binary phenotypes from DIRAC paper
phenotypesLevels - A factor for binary phenotypes from DIRAC paper
phenotypesLevels - A factor for binary phenotypes from DIRAC paper
phenotypesLevels - A factor for binary phenotypes from DIRAC paper
phenotypesLevels - A factor for binary phenotypes from DIRAC paper
phenotypesLevels - A factor for binary phenotypes from DIRAC paper
phenotypesLevels - A factor for binary phenotypes from DIRAC paper
phenotypesLevels - A factor for binary phenotypes from DIRAC paper
phenotypesLevels - A factor for binary phenotypes from DIRAC paper
phenotypesLevels - A factor for binary phenotypes from DIRAC paper

On BioConductor:GSBenchMark-1.33.0(data/experiment 3.24)GSBenchMark-1.32.0(data/experiment 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarraydata datapkg

3.38 score 12 scripts 0 exports 0 dependencies

Last updated from:e1056b961e. Checks:1 ERROR, 3 OK. Indexed: yes.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	ERROR	111
linux-devel	OK	140
source / vignettes	OK	304
linux-release	OK	180

Exports:

Dependencies:

Working with the GSBenchMark package

Introduction | Datasets | System Information | Literature Cited

Rendered fromGSBenchMark.Rnwusingutils::Sweave

Last update: 2014-07-17
Started: 2014-07-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A list of pathways and 11 datasets consisting gene expressions and phenotypes as the benchmark for Gene Set Analysis. Most of this information was used to validate Differential Rank Conservation (DIRAC) in the first place. In addition the data in the Eddy et al. (2010) paper, we also provide two datasets.	GSBenchMark-package GSBenchMark
Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Bipolar	bipolar_GDS2190
Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Breast cancer	breast_GDS807
The pathways downloaded from DIRAC paper	diracpathways
Gene expression matrix from DIRAC paper	exprsdata
The names of the datasets of gene expressions and phenotypes downloaded from DIRAC paper	GSBenchMark.Dataset.names GSBenchMarkDatasets
Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Leukaemia	leukemia_GSEA
Gene expression matrix from DIRAC paper	logexprsdata
Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Marfan	marfan_GDS2960
Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Melanoma	melanoma_GDS2735
Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Parkinson's	parkinsons_GDS2519
A factor for binary phenotypes from DIRAC paper	phenotypes phenotypesLevels
Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Prostate	prostate_GDS2545_m_nf
Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Prostate	prostate_GDS2545_m_p
Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Prostate	prostate_GDS2545_p_nf
Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Sarcoma	sarcoma_data
Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Squamous (Head and Neck Cancer)	squamous_GDS2520