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psSubpathway
View on CRAN: Click
here
Download and install psSubpathway package within the R console
Install from CRAN:
install.packages("psSubpathway")
Install from Github:
library("remotes")
install_github("cran/psSubpathway")
Install by package version:
library("remotes")
install_version("psSubpathway", "0.1.3")
Attach the package and use:
library("psSubpathway")
Maintained by
Junwei Han
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-06-21
Latest Update: 2023-08-09
Description:
A network-based systems biology tool for flexible identification of phenotype-specific subpathways in the cancer gene expression data
with multiple categories (such as multiple subtype or developmental stages of cancer). Subtype Set Enrichment Analysis (SubSEA) and Dynamic Changed
Subpathway Analysis (DCSA) are developed to flexible identify subtype specific and dynamic changed subpathways respectively. The operation modes
include extraction of subpathways from biological pathways, inference of subpathway activities in the context of gene expression data, identification
of subtype specific subpathways with SubSEA, identification of dynamic changed subpathways associated with the cancer developmental stage with DCSA,
and visualization of the activities of resulting subpathways by using box plots and heat maps. Its capabilities render the tool could find the specific
abnormal subpathways in the cancer dataset with multi-phenotype samples.
How to cite:
Junwei Han (2019). psSubpathway: Flexible Identification of Phenotype-Specific Subpathways. R package version 0.1.3, https://cran.r-project.org/web/packages/psSubpathway
Previous versions and publish date:
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Other R packages that psSubpathway depends,
imports, suggests or enhances
Functions, R codes and Examples using
the psSubpathway R package
Some associated functions: DCSA . FastSEAscore . ReadClsFile . SEAscore . SubSEA . compute_rank_score . envData . getgenedensity . isPackageLoaded . ks_test_m . plotSpwACmap . plotSpwNetmap . plotSpwPSheatmap . plotSubSEScurve . plotheatmap . rndWalk . ssgsea .
Some associated R codes: DCSAcs.R . FastSEAscore.R . ReadClsFile.R . SEAscore.R . SubSEA.R . compute_rank_score.R . getgenedensity.R . isPackageLoaded.R . ks_test_m.R . plotSpwACmap.R . plotSpwNetmap.R . plotSpwPSheatmap.R . plotSubSEScurve.R . plotheatmap.R . rndWalk.R . ssgsea.R . Full psSubpathway package functions and examples
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