Package: padma 1.17.0
Andrea Rau
padma: Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Use multiple factor analysis to calculate individualized pathway-centric scores of deviation with respect to the sampled population based on multi-omic assays (e.g., RNA-seq, copy number alterations, methylation, etc). Graphical and numerical outputs are provided to identify highly aberrant individuals for a particular pathway of interest, as well as the gene and omics drivers of aberrant multi-omic profiles.
Authors:
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padma.pdf |padma.html✨
padma/json (API)
NEWS
| # Install 'padma' in R: |
| install.packages('padma', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/andreamrau/padma/issues
- LUAD_subset - Subset of batch-corrected multi-omic TCGA data in lung adenocarcinoma
- mirtarbase - Curated miR-target interaction predictions from miRTarBase
- msigdb - MSigDB canonical pathways and corresponding gene lists
On BioConductor:padma-1.15.1(bioc 3.20)padma-1.14.1(bioc 3.19)
softwarestatisticalmethodprincipalcomponentgeneexpressionpathwaysrnaseqbiocartamethylseq
Last updated 23 days agofrom:816cd17e34. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | OK | Oct 31 2024 |
| R-4.5-linux | OK | Oct 30 2024 |
| R-4.4-win | OK | Oct 31 2024 |
| R-4.4-mac | OK | Oct 31 2024 |
| R-4.3-win | OK | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:factorMapimputed_genesMFA_resultsngenesomicsContribpadmapadmaRunpathway_gene_deviationpathway_nameremoved_genesshow
Dependencies:abindaskpassbackportsbase64encBiobaseBiocBaseUtilsBiocGenericsbootbroombslibcachemcarcarDatacliclustercolorspacecowplotcpp11crayoncrosstalkcurlDelayedArrayDerivdigestdoBydplyrDTellipseemmeansestimabilityevaluateFactoMineRfansifarverfastmapflashClustfontawesomeFormulafsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleapslifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewMultiAssayExperimentmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigpromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownS4ArraysS4Vectorssassscalesscatterplot3dSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Plot an MFA factor map for individuals or partial factor map based on padma analysis | factorMap |
| Subset of batch-corrected multi-omic TCGA data in lung adenocarcinoma | LUAD_subset |
| Curated miR-target interaction predictions from miRTarBase | mirtarbase |
| MSigDB canonical pathways and corresponding gene lists | msigdb |
| Plot the omics contribution per MFA axis and the overall weighted contribution | omicsContrib |
| Calculate individualized deviation scores from multi-omic data | padma padma,list-method padma,MultiAssayExperiment-method padma-methods |
| padmaResults object and constructor | padmaResults padmaResults-class |
| Calculate individualized deviation scores from multi-omic data | padmaRun |
| Accessors for a padmaResults object. | imputed_genes imputed_genes,padmaResults-method MFA_results MFA_results,padmaResults-method ngenes ngenes,padmaResults-method pathway_gene_deviation pathway_gene_deviation,padmaResults-method pathway_gene_deviation-method pathway_name pathway_name,padmaResults-method removed_genes removed_genes,padmaResults-method show show,padmaResults-method |
| Summarize results from padma | summary summary,padmaResults-method summary-methods |
