Introduction | Installation | PICtR Pipeline | Pre-Processing of Cytometry Data | Example Data | Subsampling, Dimensional Reduction and Clustering | Guidelines for Clustering | Predict Labels for the full Data Set | Selecting Interacting Populations | Singlet Annotation | Annotation of Interacting Populations | Downstream Analysis | Citing PICtR | References
Package: PICtR 1.0.2
Viktoria Flore
PICtR: Physically Interacting Cell (PIC) toolkit for R
This is the computational workflow to analyse physically interacting cells (PICs) in flow cytometry data using R.
Authors:
PICtR_1.0.2.tar.gz
PICtR_1.0.2.zip(r-4.7-any)PICtR_1.0.2.zip(r-4.6-any)PICtR_1.0.2.zip(r-4.5-any)
PICtR_1.0.2.tgz(r-4.6-any)PICtR_1.0.2.tgz(r-4.5-any)
PICtR_1.0.2.tar.gz(r-4.7-any)PICtR_1.0.2.tar.gz(r-4.6-any)
PICtR_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
PICtR/json (API)
| # Install 'PICtR' in R: |
| install.packages('PICtR', repos = c('https://agshaas.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/agshaas/pictr/issues
Pkgdown/docs site:https://agshaas.github.io
Datasets:
- demo_lcmv - Demo data set
Last updated from:b2b88db127. Checks:7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | WARNING | 300 | ||
| source / vignettes | OK | 449 | ||
| linux-release | WARNING | 317 | ||
| macos-release | WARNING | 336 | ||
| macos-oldrel | WARNING | 306 | ||
| windows-devel | WARNING | 252 | ||
| windows-release | WARNING | 238 | ||
| windows-oldrel | WARNING | 342 | ||
| wasm-release | OK | 200 |
Exports:calculateThresholdimport_cytometry_dataMEM_heatmappredict_dataratio_cluster_plotsave.objsave.plotselect_dbtsketch_wrappersplit_plot_sketchumap_rasterizedwrapper_for_plots
Dependencies:abindaskpassbase64encBHbitbit64bitopsBPCellsbslibcachemcaToolsclicliprclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdichromatdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehexbinhighrhmshtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothkhromaknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagrittrmapprojmapsMASSMatrixmatrixStatsmemoisemimeminiUInlmeopensslotelpalsparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprettyunitsprogressprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppThreadRcppTOMLreadrreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS7sassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytextzdbutf8uwotvctrsviridisLitevroomwithrxfunxtableyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Threshold calculation | calculateThreshold |
| Demo data set | demo_lcmv |
| Data Import Helper | import_cytometry_data |
| Marker Enrichment Modeling (MEM) Heatmap. | MEM_heatmap |
| Cluster label prediction | predict_data |
| Ratio cluster plot. | ratio_cluster_plot |
| Save Seurat object | save.obj |
| Save plot | save.plot |
| Selection of clusters containing physically interacting cells. | select_dbt |
| PICtR workflow wrapper | sketch_wrapper |
| Split plot wrapper. | split_plot_sketch |
| Rasterized UMAP | umap_rasterized |
| Plot wrapper function. | wrapper_for_plots |