Package: consICA 2.3.0
Petr V. Nazarov
consICA: consensus Independent Component Analysis
consICA implements a data-driven deconvolution method – consensus independent component analysis (ICA) to decompose heterogeneous omics data and extract features suitable for patient diagnostics and prognostics. The method separates biologically relevant transcriptional signals from technical effects and provides information about the cellular composition and biological processes. The implementation of parallel computing in the package ensures efficient analysis of modern multicore systems.
Authors:
consICA_2.3.0.tar.gz
consICA_2.3.0.zip(r-4.5)consICA_2.3.0.zip(r-4.4)consICA_2.3.0.zip(r-4.3)
consICA_2.3.0.tgz(r-4.4-any)consICA_2.3.0.tgz(r-4.3-any)
consICA_2.3.0.tar.gz(r-4.5-noble)consICA_2.3.0.tar.gz(r-4.4-noble)
consICA_2.3.0.tgz(r-4.4-emscripten)consICA_2.3.0.tgz(r-4.3-emscripten)
consICA.pdf |consICA.html✨
consICA/json (API)
NEWS
| # Install 'consICA' in R: |
| install.packages('consICA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/biomod-lih/consica/issues
- samples_data - Samples of gene expression
On BioConductor:consICA-2.3.0(bioc 3.20)consICA-2.2.0(bioc 3.19)
Last updated 2 months agofrom:6227be0703
Exports:anovaICconsICAestimateVarianceExplainedgetFeaturesgetGOis.consICAoneICAoverlapGOplotICVarianceExplainedsaveReportsetOrientationsortDataFramesurvivalAnalysis
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArrayfansifarverfastICAfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2glueGO.dbgraphgtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dbpheatmappillarpkgconfigplogrpngR6RColorBrewerRcppRcppArmadilloRcppGSLRcppParallelRcppZigguratRfastrlangRSQLiteS4ArraysS4VectorsscalessmsnowSparseArraySparseMSummarizedExperimentsurvivalsystibbletopGOUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ANOVA test for independent component across factors | anovaIC |
| Calculate consensus Independent Component Analysis | consICA |
| Enrichment analysis of GO-terms based on Ensembl IDs | enrichGO |
| Estimate the variance explained by the model | estimateVarianceExplained |
| Get features from consICA deconvolution result | getFeatures |
| Assigns IC signatures to Gene Ontologies | getGO |
| Is the object is consensus ICA compliant? | is.consICA |
| Runs 'fastICA' | oneICA |
| Similarity of two gene ontologies lists | overlapGO |
| Barplot variance explained by each IC | plotICVarianceExplained |
| Samples of gene expression | samples_data |
| Save PDF report with analysis of each independent component | saveReport |
| Set orientation for independent components | setOrientation |
| Sort dataframe | sortDataFrame |
| Survival analysis based on significant IC | survivalAnalysis |
