Flexible Identification of Phenotype-Specific Subpathways
Overview
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.
Install
Health
ERRORpackage dependenciesr-patched-linux-x86_64
Package required but not available: ‘GSVA’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Maintainer: ‘Junwei Han <hanjunwei1981@163.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Xudong",
family = "Han",
role = "aut"),
person(given = "Junwei",
family = "Han",
role = c("aut", "cre"),
email = "hanjunwei1981@163.com"),
person(given = "Qing",
family = "Fei",
role = "aut"))
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Documentation
- Help pages
- 17
- Examples that run
- 100%7 run in a plain check
- Exported functions with examples
- 78%
- Documented parameters
- 100%
- Return-value docs
- 78%
- Help pages citing references
- 0%
Downloads
Dependencies
Installing psSubpathway adds 18 packages (8 with compiled code, 11 MB of source tarballs). Heaviest: igraph 4.8 MB, farver 1.2 MB, viridisLite 1.2 MB. 1 more not on CRAN is not measured.
Code & Tests
Datasets
People & History
Maintainer since 0.1.0 (2019)
Pick two releases to compare their code metrics.
- RR 4.6.0 released · 2026-04-24
- RR 4.5.0 released · 2025-04-11
- RR 4.4.0 released · 2024-04-24
- 0.1.3Latest
- 0.1.22023-08-09 · diff ↗
- RR 4.3.0 released · 2023-04-21
- RR 4.2.0 released · 2022-04-22
- RR 4.1.0 released · 2021-05-18
- RR 4.0.0 released · 2020-04-24
- 0.1.1
- 0.1.02019-06-21
- RR 3.6.0 released · 2019-04-26
Package metadata
- First published
- 2019-06-21
- Total releases
- 4 / 7 yrs
- License
- GPL (>= 2) OSI
- Minimum R
- ≥ 3.5.0
- Bundled data
- 3.2 MB / 9 files
- Download size
- 3.4 MB
Cite
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