Package: DysPIA 1.4

DysPIA: Dysregulated Pathway Identification Analysis

It is used to identify dysregulated pathways based on a pre-ranked gene pair list. A fast algorithm is used to make the computation really fast. The data in package 'DysPIAData' is needed.

Authors:Limei Wang [aut, cre], Jin Li [aut, ctb]

DysPIA_1.4.tar.gz
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DysPIA_1.4.tgz(r-4.4-x86_64)DysPIA_1.4.tgz(r-4.4-arm64)DysPIA_1.4.tgz(r-4.3-x86_64)DysPIA_1.4.tgz(r-4.3-arm64)
DysPIA_1.4.tar.gz(r-4.5-noble)DysPIA_1.4.tar.gz(r-4.4-noble)
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DysPIA.pdf |DysPIA.html✨
DysPIA/json (API)

# Install 'DysPIA' in R:

install.packages('DysPIA', repos = c('https://lemonwang2020.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lemonwang2020/dyspia/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

DysGPS_p53 - Example vector of DysGPS in p53 data.
DyspiaRes_p53 - Example list of DysPIA result in p53 data.
class.labels_p53 - Example vector of category labels.
gene_expression_p53 - Example matrix of gene expression value.
sample_background - Example list of gene pair background.

On CRAN:

2.70 score 228 downloads 1 mentions 9 exports 14 dependencies

Last updated 4 years agofrom:b15711bbb9. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 07 2024
R-4.5-win-x86_64	OK	Nov 07 2024
R-4.5-linux-x86_64	OK	Nov 07 2024
R-4.4-win-x86_64	OK	Nov 07 2024
R-4.4-mac-x86_64	OK	Nov 07 2024
R-4.4-mac-aarch64	OK	Nov 07 2024
R-4.3-win-x86_64	OK	Nov 07 2024
R-4.3-mac-x86_64	OK	Nov 07 2024
R-4.3-mac-aarch64	OK	Nov 07 2024

Exports:calcDyspiaStat calcDyspiaStatCumulative calcDyspiaStatCumulativeBatch calEdgeCorScore_ESEA DysGPS DysPIA DyspiaSig DyspiaSimpleImpl setUpBPPARAM

Dependencies:BH BiocParallel codetools cpp11 data.table DysPIAData fastmatch FNN formatR futile.logger futile.options lambda.r Rcpp snow

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
calcDyspiaStat: Calculates DysPIA statistics	calcDyspiaStat
Calculates DysPIA statistic values for all the prefixes of a gene pair set	calcDyspiaStatCumulative
Calculates DysPIA statistic values for the gene pair sets	calcDyspiaStatCumulativeBatch
calEdgeCorScore_ESE	calEdgeCorScore_ESEA
Example vector of category labels.	class.labels_p53
DysGPS: Calculates Dysregulated gene pair score (DysGPS) for each gene pair	DysGPS
Example vector of DysGPS in p53 data.	DysGPS_p53
DysPIA: Dysregulated Pathway Identification Analysis	DysPIA
Example list of DysPIA result in p53 data.	DyspiaRes_p53
DyspiaSig	DyspiaSig
DyspiaSimpleImpl	DyspiaSimpleImpl
Example matrix of gene expression value.	gene_expression_p53
Example list of gene pair background.	sample_background
setUpBPPARAM	setUpBPPARAM