Environment setup | 1. Load and Prepare CRC Dataset | 2. Differential Expression Analysis | 3. Label-Switch Classification | 4. UMAP Visualization of Feature Subsets | 5. Quadrant Assignment and Delta–Fold-Change Scatter Plot | 6. Expression Patterns of Representative Features | 7. Heatmap of Quadrant-Defined Features | 8. Pathway Enrichment Analysis (Reactome) | Session information
Package: SwitchClass 0.99.1
Di Xiao
SwitchClass: Label-Switch Classification for Baseline- and Perturbation-Aligned Features
Quantifies baseline-aligned and perturbation-aligned molecular features across biological perturbations using a label-switch classification framework. Provides a unified workflow for identifying changes in molecular-feature alignment in longitudinal or comparative omics datasets. Includes tools for classification, visualization, dimension reduction, and pathway enrichment.
Authors:
SwitchClass_0.99.1.tar.gz
SwitchClass_0.99.1.zip(r-4.7-any)SwitchClass_0.99.1.zip(r-4.6-any)SwitchClass_0.99.1.zip(r-4.5-any)
SwitchClass_0.99.1.tgz(r-4.6-any)SwitchClass_0.99.1.tgz(r-4.5-any)
SwitchClass_0.99.1.tar.gz(r-4.7-any)SwitchClass_0.99.1.tar.gz(r-4.6-any)
SwitchClass_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SwitchClass/json (API)
| # Install 'SwitchClass' in R: |
| install.packages('SwitchClass', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/pyanglab/switchclass/issues
Datasets:
- CRC_subset - CRC subset data
softwareclassificationfeatureextractiongeneexpressionproteomicstranscriptomicssinglecellpathways
Last updated from:106a48d811. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 296 | ||
| linux-devel | OK | 231 | ||
| source / vignettes | OK | 435 | ||
| linux-release | OK | 291 | ||
| macos-release | OK | 178 | ||
| macos-oldrel | OK | 179 | ||
| windows-devel | OK | 179 | ||
| windows-release | OK | 170 | ||
| windows-oldrel | OK | 187 | ||
| wasm-release | OK | 281 |
Exports:assign_quadrantsenrich_reactome_quadrantslabel_switch_classifyplot_delta_vs_fcplot_feature_boxplotsplot_heatmap_quadrantsplot_umaprun_umap_samplesumap_triptych_by_delta
Dependencies:abindbackportsBHBiobaseBiocGenericsbootbroomcarcarDatacirclizeclassclicodacolorspacecommonmarkcorrplotcowplotcpp11crayoncurlDelayedArraydendextendDerivdoBydplyrdqrnge1071farverFNNforcatsforecastFormulafracdiffgenericsGenomicRangesGGallyggdendroggplot2ggpubrggrepelggsciggsignifggstatsggtextGlobalOptionsgluegridExtragridtextgtablehmsigraphIRangesirlbaisobandjpeglabelinglatticelifecyclelimmalitedownlme4lmtestmagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvminqamodelrnetworknlmenloptrnnetnumDerivpatchworkpbkrtestpcaMethodspheatmapPhosRpillarpkgconfigplyrpngpolynompreprocessCoreprettyunitsprogressproxypurrrquantregR6randomForestrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressRdpackreformulasreshape2rlangRSpectrarstatixruvS4ArraysS4VectorsS7scalesSeqinfoshapesitmoSparseArraySparseMstatmodstatnet.commonstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttimeDateurcautf8uwotvctrsviridisviridisLitewithrxfunxml2XVectorzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Assign SwitchClass quadrants | assign_quadrants |
| CRC subset data | CRC_subset |
| Reactome ORA per quadrant | enrich_reactome_quadrants |
| Label-switch classification (with optional multicore) | label_switch_classify |
| Scatter plot of delta vs fold-change with quadrant assignment | plot_delta_vs_fc |
| Boxplots for selected features across groups | plot_feature_boxplots |
| Plot heatmap for quadrant-classified features | plot_heatmap_quadrants |
| Quick ggplot for UMAP embedding | plot_umap |
| UMAP on samples using selected features | run_umap_samples |
| UMAP triptych using delta-ranked features | umap_triptych_by_delta |