Package: ssPATHS 1.21.0
Natalie R. Davidson
ssPATHS: ssPATHS: Single Sample PATHway Score
This package generates pathway scores from expression data for single samples after training on a reference cohort. The score is generated by taking the expression of a gene set (pathway) from a reference cohort and performing linear discriminant analysis to distinguish samples in the cohort that have the pathway augmented and not. The separating hyperplane is then used to score new samples.
Authors:
ssPATHS_1.21.0.tar.gz
ssPATHS_1.21.0.zip(r-4.5)ssPATHS_1.21.0.zip(r-4.4)ssPATHS_1.21.0.zip(r-4.3)
ssPATHS_1.21.0.tgz(r-4.4-any)ssPATHS_1.21.0.tgz(r-4.3-any)
ssPATHS_1.21.0.tar.gz(r-4.5-noble)ssPATHS_1.21.0.tar.gz(r-4.4-noble)
ssPATHS_1.21.0.tgz(r-4.4-emscripten)ssPATHS_1.21.0.tgz(r-4.3-emscripten)
ssPATHS.pdf |ssPATHS.html✨
ssPATHS/json (API)
| # Install 'ssPATHS' in R: |
| install.packages('ssPATHS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- expected_score_output - Gene Expression Values for PDAC Cancer Cell Lines exposed to Hypoxia
- gene_weights_reference - Gene Expression Values for PDAC Cancer Cell Lines exposed to Hypoxia
- new_samp_df - Gene Expression Values for PDAC Cancer Cell Lines exposed to Hypoxia
- tcga_expr_df - Gene Expression Values for PDAC Cancer Cell Lines exposed to Hypoxia
On BioConductor:ssPATHS-1.21.0(bioc 3.21)ssPATHS-1.20.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwaregeneexpressionbiomedicalinformaticsrnaseqpathwaystranscriptomicsdimensionreductionclassification
Last updated 2 months agofrom:bd3f81eeb2. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | OK | Nov 30 2024 |
| R-4.5-linux | OK | Nov 30 2024 |
| R-4.4-win | OK | Nov 30 2024 |
| R-4.4-mac | OK | Nov 30 2024 |
| R-4.3-win | OK | Nov 30 2024 |
| R-4.3-mac | OK | Nov 30 2024 |
Exports:get_classification_accuracyget_gene_weightsget_hypoxia_genesget_new_samp_score
Dependencies:abindaskpassbackportsBiobaseBiocGenericsbitbit64bitopsbroomcaToolsclicliprcodetoolscolorspacecpp11crayoncurlDelayedArraydmldplyrevaluatefansifarverforcatsforeachgeeMgeepackgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggformulaggplot2ggridgesglmnetgluegplotsgtablegtoolshavenhighrhmshttrIRangesisobanditeratorsjsonliteKernSmoothkinship2knitrlabelinglabelledlatticelfdalifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsMESSmgcvmimemosaicCoremunsellmvtnormnlmeopensslpillarpkgconfigplyrprettyunitsprogresspurrrquadprogR6rARPACKRColorBrewerRcppRcppArmadilloRcppEigenreadrrlangROCRRSpectraS4ArraysS4VectorsscalesshapeSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gene Expression Values for PDAC Cancer Cell Lines exposed to Hypoxia | expected_score_output |
| Gene Expression Values for PDAC Cancer Cell Lines exposed to Hypoxia | gene_weights_reference |
| Get Classification Accuracy | get_classification_accuracy |
| Get Gene Weights from Reference Data | get_gene_weights |
| Get Ensembl ids of hypoxia related genes. | get_hypoxia_genes |
| Get a pathway score for an unseen sample | get_new_samp_score |
| Gene Expression Values for PDAC Cancer Cell Lines exposed to Hypoxia | new_samp_df |
| Gene Expression Values for PDAC Cancer Cell Lines exposed to Hypoxia | tcga_expr_df |
