Package: piano 2.23.0
Leif Varemo Wigge
piano: Platform for integrative analysis of omics data
Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.
Authors:
piano_2.23.0.tar.gz
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piano_2.23.0.tgz(r-4.4-any)piano_2.23.0.tgz(r-4.3-any)
piano_2.23.0.tar.gz(r-4.5-noble)piano_2.23.0.tar.gz(r-4.4-noble)
piano_2.23.0.tgz(r-4.4-emscripten)piano_2.23.0.tgz(r-4.3-emscripten)
piano.pdf |piano.html✨
piano/json (API)
NEWS
| # Install 'piano' in R: |
| install.packages('piano', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/varemo/piano/issues
- gsa_input - Random input data for gene set analysis
- gsa_results - Gene set analysis result data
On BioConductor:piano-2.23.0(bioc 3.21)piano-2.22.0(bioc 3.20)
microarraypreprocessingqualitycontroldifferentialexpressionvisualizationgeneexpressiongenesetenrichmentpathwaysbioconductorbioconductor-packagebioinformaticsgene-set-enrichmenttranscriptomics
Last updated 25 days agofrom:f5e29d0a18. Checks:ERROR: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Oct 31 2024 |
| R-4.5-win | WARNING | Oct 31 2024 |
| R-4.5-linux | WARNING | Oct 31 2024 |
| R-4.4-win | WARNING | Oct 31 2024 |
| R-4.4-mac | WARNING | Oct 31 2024 |
| R-4.3-win | WARNING | Oct 31 2024 |
| R-4.3-mac | WARNING | Oct 31 2024 |
Exports:consensusHeatmapconsensusScoresdiffExpexploreGSAresextractFactorsgeneSetSummaryGSAheatmapGSAsummaryTableloadGSCloadMAdatanetworkPlotnetworkPlot2polarPlotrunGSArunGSAhyperrunQCwriteFilesForKiwi
Dependencies:base64encBHBiobaseBiocGenericsBiocParallelbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkdata.tabledigestDTevaluatefansifarverfastmapfastmatchfgseafontawesomeformatRfsfutile.loggerfutile.optionsggplot2gluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttpuvigraphisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrmarrayMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigpromisesR6rappdirsRColorBrewerRcpprelationsrlangrmarkdownsassscalessetsshinyshinydashboardshinyjsslamsnowsourcetoolsstatmodtibbletinytexutf8vctrsviridisLitevisNetworkwithrxfunxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Piano - Platform for Integrative ANalysis of Omics data | piano-package piano |
| Heatmap of top consensus gene sets | consensusHeatmap |
| Top consensus gene sets and boxplot | consensusScores |
| Perform differential expression analysis | diffExp |
| Explore GSA results | exploreGSAres |
| Extracts 'ArrayData' factors | extractFactors |
| Gene set summary | geneSetSummary |
| Random input data for gene set analysis | gsa_input |
| Gene set analysis result data | gsa_results |
| Heatmap of top significant gene sets | GSAheatmap |
| Gene set analysis summary table | GSAsummaryTable |
| Load a gene set collection | loadGSC |
| Load and preprocess microarray data | loadMAdata |
| Gene set network plot | networkPlot |
| Gene set network plot | networkPlot2 |
| Polar plot | polarPlot |
| Gene set analysis | runGSA |
| Gene set analysis with Fisher's exact test | runGSAhyper |
| Run quality control | runQC |
| Write files for Kiwi | writeFilesForKiwi |