Package: flowMatch 1.43.0
Ariful Azad
flowMatch: Matching and meta-clustering in flow cytometry
Matching cell populations and building meta-clusters and templates from a collection of FC samples.
Authors:
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flowMatch.pdf |flowMatch.html✨
flowMatch/json (API)
| # Install 'flowMatch' in R: |
| install.packages('flowMatch', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:flowMatch-1.41.0(bioc 3.20)flowMatch-1.40.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyclusteringflowcytometry
Last updated 26 days agofrom:8cc0506629. Checks:OK: 1 NOTE: 2 ERROR: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win-x86_64 | ERROR | Oct 30 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 30 2024 |
| R-4.4-win-x86_64 | NOTE | Oct 30 2024 |
| R-4.4-mac-x86_64 | ERROR | Oct 30 2024 |
| R-4.4-mac-aarch64 | ERROR | Oct 30 2024 |
| R-4.3-win-x86_64 | ERROR | Oct 30 2024 |
| R-4.3-mac-x86_64 | ERROR | Oct 30 2024 |
| R-4.3-mac-aarch64 | ERROR | Oct 30 2024 |
Exports:ClusterClusteredSamplecreate.templatedist.clusterdist.matrixdist.sampledist.templateget.centerget.cluster.idget.clustersget.covget.dimensionget.labelsget.match12get.match21get.matching.costget.metaClustersget.num.clustersget.num.metaclustersget.sample.idget.sizeget.template.idget.treeget.unmatch.penaltymahalanobis.distmatch.clustersmatch.clusters.distMetaClusterplotsample.id<-summarysymmetric.KLTemplatetemplate.tree
Dependencies:BHBiobaseBiocGenericscpp11cytolibflowCorematrixStatsRcppRhdf5libRProtoBufLibS4Vectors
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Matching cell populations and building meta-clusters and templates from a collection of FC samples. | flowMatch-package flowMatch |
| Cluster: A class representing a cell population in FC | Cluster Cluster-class get.center get.center,Cluster-method get.cluster.id get.cluster.id,Cluster-method get.cov get.cov,Cluster-method get.sample.id get.sample.id,Cluster-method get.size get.size,Cluster-method sample.id<- sample.id<-,Cluster-method show,Cluster-method summary,Cluster-method |
| ClusteredSample: A class representing a clustered FC Sample | ClusteredSample ClusteredSample-class get.clusters get.clusters,ClusteredSample-method get.dimension get.dimension,ClusteredSample-method get.labels get.labels,ClusteredSample-method get.num.clusters get.num.clusters,ClusteredSample-method get.sample.id,ClusteredSample-method get.size,ClusteredSample-method plot,ANY,ClusteredSample-method plot,flowFrame,ClusteredSample-method show,ClusteredSample-method summary,ClusteredSample-method |
| ClusterMatch: A class representing matching of cluster/meta-clusters across a pair of FC samples/templates | ClusterMatch ClusterMatch-class get.match12 get.match12,ClusterMatch-method get.match21 get.match21,ClusterMatch-method get.matching.cost get.matching.cost,ClusterMatch-method get.unmatch.penalty get.unmatch.penalty,ClusterMatch-method show,ClusterMatch-method summary,ClusterMatch-method |
| Creating a template of a collection of FC samples | create.template |
| Dissimilarity between a pair of clusters | dist.cluster |
| Dissimilarity matrix between each pair of clusters/meta-clusters across a pair of samples/templates | dist.matrix |
| Dissimilarity between a pair of clustered FC samples | dist.sample |
| Dissimilarity between a pair of FC templates | dist.template |
| Mahanalobis Distance | mahalanobis.dist |
| Matching of clusters/meta-clusters across FC samples/templates | match.clusters match.clusters.dist |
| MetaCluster: An S4 class representing a meta-cluster (collection of biologically similar clusters). | get.center,MetaCluster-method get.clusters,MetaCluster-method get.cov,MetaCluster-method get.num.clusters,MetaCluster-method get.size,MetaCluster-method MetaCluster MetaCluster-class plot,MetaCluster,missing-method plot,MetaCluster-method show,MetaCluster-method summary,MetaCluster-method |
| Symmetrized Kullback-Leibler divergence | symmetric.KL |
| Template: An S4 class representing a template of a group of FC Samples. | get.dimension,Template-method get.metaClusters get.metaClusters,Template-method get.num.metaclusters get.num.metaclusters,Template-method get.size,Template-method get.template.id get.template.id,Template-method get.tree get.tree,Template-method plot,Template,ANY-method plot,Template,missing-method plot,Template-method show,Template-method summary,Template-method Template Template-class |
| Plot the hierarchy of samples established while creating a template-tree | template.tree template.tree,Template-method |