Package: GSDA 1.0

GSDA: Gene Set Distance Analysis (GSDA)

The gene-set distance analysis of omic data is implemented by generalizing distance correlations to evaluate the association of a gene set with categorical and censored event-time variables.

Authors:Xueyuan Cao [aut, cre], Stanley Pounds [aut]

GSDA_1.0.tar.gz
GSDA_1.0.zip(r-4.7-any)GSDA_1.0.zip(r-4.6-any)GSDA_1.0.zip(r-4.5-any)
GSDA_1.0.tgz(r-4.6-any)GSDA_1.0.tgz(r-4.5-any)
GSDA_1.0.tar.gz(r-4.7-any)GSDA_1.0.tar.gz(r-4.6-any)
GSDA_1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GSDA/json (API)

# Install 'GSDA' in R:

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

Bug tracker:https://github.com/xueyuancao/gsda/issues

Datasets:

kegg.ml.gsets - KEGG gene set data for the AML and CML pathways
target.aml.clin - Clinical outcomes for AML TARGET Project
target.aml.expr - RNA-seq expression from the AML TARGET project

On CRAN:

microarray bioinformatics gene expression

4.30 score 1 stars 10 scripts 405 downloads 4 mentions 10 exports 19 dependencies

Last updated from:d7f71cb8b7. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	109
source / vignettes	OK	232
linux-release	OK	164
macos-release	OK	147
macos-oldrel	OK	128
windows-devel	OK	70
windows-release	OK	71
windows-oldrel	OK	55
wasm-release	OK	94

Exports:best.dist.corr cat.dist dist.corr gsda prep.gsda prep.msigdb surv.dist U.center uc.dist write.gsda.csv.file

Dependencies:assertthat babelgene cli curl dplyr generics glue lifecycle magrittr msigdbr pillar pkgconfig R6 rlang tibble tidyselect utf8 vctrs withr

An Introduction to the GSDA Package

Rendered fromGSDA.Rmdusingknitr::rmarkdown

Last update: 2021-01-14
Started: 2020-06-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Gene Set Distance Analysis (GSDA)	GSDA-package GSDA
Best Distance Correlattion	best.dist.corr
Distance for a Categorical Variable	cat.dist
Distance Correlattion	dist.corr
Gene-Set Distance Analsysis (GSDA)	gsda
KEGG gene set data for the AML and CML pathways	kegg.ml.gsets
GSDA Data Preparation	prep.gsda
Preparation of MSigDB for GSDA	prep.msigdb
Print Method for Best Distance Correlation	print.bdc
Print Method for Distance Correlation	print.dcor
Print Method for GSDA Result	print.gsda.result
Distance of a Survival Endpoint	surv.dist
Clinical outcomes for AML TARGET Project	target.aml.clin
RNA-seq expression from the AML TARGET project	target.aml.expr
U Centering	U.center
U-centered Distance Matrix	uc.dist
Write GSDA Result to a Comma Delimited File	write.gsda.csv.file