Introduction | Demonstration dataset | Input and clustering | Run MacrophageFramework | Macrophage detection | Manually specifying macrophage clusters | Multidimensional program profiles | Program intensity (score) | Program coverage | Program coherence | Similarity between cluster profiles | Visual summaries | Original computational clusters | Multidimensional framework annotation | Program intensity | Alternative input: expression matrix and cluster assignments | Outputs and interpretation | Reproducibility and limitations | Session information
Package: MacrophageFramework 0.99.0
Alessandro Palma
MacrophageFramework: Multidimensional Macrophage Profiling
Provides a multidimensional computational framework for macrophage profiling based on an ontology of biological programs. The framework independently detects macrophage populations and characterizes their lineage-associated and functional-state programs using program-level expression scores, detection coverage, gene-program coherence, cluster profiles, and profile similarity. The framework is designed to capture continuous and combinatorial macrophage states without imposing binary activation categories.
Authors:
MacrophageFramework_0.99.0.tar.gz
MacrophageFramework_0.99.0.zip(r-4.7-any)MacrophageFramework_0.99.0.zip(r-4.6-any)MacrophageFramework_0.99.0.zip(r-4.5-any)
MacrophageFramework_0.99.0.tgz(r-4.6-any)MacrophageFramework_0.99.0.tgz(r-4.5-any)
MacrophageFramework_0.99.0.tar.gz(r-4.7-any)MacrophageFramework_0.99.0.tar.gz(r-4.6-any)
MacrophageFramework_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MacrophageFramework/json (API)
| # Install 'MacrophageFramework' in R: |
| install.packages('MacrophageFramework', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/alessandropalma-hub/macrophageframework/issues
geneexpressionimmunooncologysinglecellsoftwarevisualization
Last updated from:3408280351. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 312 | ||
| linux-devel | OK | 197 | ||
| source / vignettes | OK | 353 | ||
| linux-release | OK | 321 | ||
| macos-release | OK | 150 | ||
| macos-oldrel | OK | 140 | ||
| windows-devel | OK | 120 | ||
| windows-release | OK | 314 | ||
| windows-oldrel | OK | 128 | ||
| wasm-release | OK | 243 |
Exports:analyze_macrophage_profilecalculate_detection_coveragecalculate_profile_similaritycalculate_program_coherenceload_ontologyplot_macrophage_profileplot_macrophage_similarityplot_macrophage_umapscore_programssummarize_macrophage_profile
Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscommonmarkcowplotcpp11crosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppThreadRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS7sassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Analyze a macrophage expression profile | analyze_macrophage_profile |
| Calculate program detection coverage | calculate_detection_coverage |
| Calculate similarity between macrophage profiles | calculate_profile_similarity |
| Calculate program coherence | calculate_program_coherence |
| Load the macrophage ontology | load_ontology |
| Plot multidimensional macrophage profiles | plot_macrophage_profile |
| Plot macrophage profile similarity | plot_macrophage_similarity |
| Plot macrophage Framework annotations on a dimensional reduction | plot_macrophage_umap |
| Score macrophage biological programs | score_programs |
| Summarize program coherence by cluster | summarize_cluster_coherence |
| Summarize macrophage profiles in a human-readable table | summarize_macrophage_profile |