Package: SPIA 2.59.0
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_2.59.0.tar.gz
SPIA_2.59.0.zip(r-4.5)SPIA_2.59.0.zip(r-4.4)SPIA_2.59.0.zip(r-4.3)
SPIA_2.59.0.tgz(r-4.4-any)SPIA_2.59.0.tgz(r-4.3-any)
SPIA_2.59.0.tar.gz(r-4.5-noble)SPIA_2.59.0.tar.gz(r-4.4-noble)
SPIA_2.59.0.tgz(r-4.4-emscripten)SPIA_2.59.0.tgz(r-4.3-emscripten)
SPIA.pdf |SPIA.html✨
SPIA/json (API)
| # Install 'SPIA' in R: |
| install.packages('SPIA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- 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-2.59.0(bioc 3.21)SPIA-2.58.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:7432fd54a8. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | NOTE | Nov 30 2024 |
| R-4.4-win | NOTE | Nov 30 2024 |
| R-4.4-mac | NOTE | Nov 30 2024 |
| R-4.3-win | NOTE | Nov 30 2024 |
| R-4.3-mac | NOTE | Nov 30 2024 |
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 |