Overview | Pathway analysis with SPIA package | Parsing up-to-date KEGG xml files for use with SPIA | Changes in SPIA 2.10 vs 2.9
Package: SPIA 2.65.0
Adi Laurentiu Tarca
SPIA: Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.
Authors:
SPIA_2.65.0.tar.gz
SPIA_2.65.0.zip(r-4.7)SPIA_2.65.0.zip(r-4.6)SPIA_2.65.0.zip(r-4.5)
SPIA_2.65.0.tgz(r-4.6-any)SPIA_2.65.0.tgz(r-4.5-any)
SPIA_2.65.0.tar.gz(r-4.7-any)SPIA_2.65.0.tar.gz(r-4.6-any)
SPIA_2.65.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SPIA/json (API)
| # Install 'SPIA' in R: |
| install.packages('SPIA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- ALL_Colorectal - Results from a microarray experiment comparing colorectal cancer samples and normal tissue samples.
- ALL_Vessels - Results from a microarray expriment comparing umbilical veins and arteries tissues
- DE_Colorectal - Results from a microarray experiment comparing colorectal cancer samples and normal tissue samples.
- DE_Vessels - Results from a microarray expriment comparing umbilical veins and arteries tissues
- top - Results from a microarray experiment comparing colorectal cancer samples and normal tissue samples.
On BioConductor:SPIA-2.65.0(bioc 3.24)SPIA-2.64.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:8b360b2502. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 175 | ||
| linux-devel-x86_64 | NOTE | 297 | ||
| source / vignettes | OK | 290 | ||
| linux-release-x86_64 | NOTE | 288 | ||
| macos-release-arm64 | NOTE | 225 | ||
| macos-oldrel-arm64 | NOTE | 241 | ||
| windows-devel | NOTE | 593 | ||
| windows-release | NOTE | 567 | ||
| windows-oldrel | NOTE | 643 | ||
| wasm-release | OK | 140 |
Exports:combfuncmakeSPIAdataplotPspia
Dependencies:BiocGenericsbitopsgenericsgraphKEGGgraphRCurlRgraphvizXML
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Results from a microarray experiment comparing colorectal cancer samples and normal tissue samples. | ALL_Colorectal colorectalcancer DE_Colorectal top |
| Combining two p-values using Fisher's product or normal inversion method | combfunc |
| Process KGML files for spia analysis | makeSPIAdata |
| SPIA two-way evidence plot | plotP |
| Signaling Pathway Impact Analysis (SPIA) based on over-representation and signaling perturbations accumulation | spia |
| Results from a microarray expriment comparing umbilical veins and arteries tissues | ALL_Vessels DE_Vessels Vessels |