| Component |
Version |
Inputs |
Outputs |
Description |
| AutoGating |
1.0 |
rule, clusters, array |
filtered, filteredArray, population, populationArray |
Automatically gate cell populations. |
| ClusterChooser |
1.0 |
population, plots, sampleAnnotation |
corrected, fileStatus |
Graphical tool for cluster population selection. |
| ClusterFiltering |
1.0 |
fcsDir, in |
filtered, out |
Filters columns and/or rows from by clusters using flexible criteria. |
| CSVListFilter |
1.0 |
clusters, populations |
filtered, array |
Filters CSV files in a given folder according to the
to extract specific rows given output of AutoGating component. |
| FCSReader |
1.0 |
in, annotations |
out, metadata |
FCSReader imports a FCS file (standards 2.0 and 3.0 supported) and
converts it into a tab-delimitted CSV file. |
| FlowClustModeling |
0.1 |
fcsDir |
clusters, report |
Modeling FACS data using flowClust library. |
| FlowMeans |
1.0 |
inList, in |
clustersList, clusters, report |
Clusters rows in CSV files. |
| GatingSummary |
1.0 |
summaries, sampleAnnotation, panel, population |
summaryResult, report |
Generate summay report table and heatmap. |
| MetaClustering |
0.1 |
optimalClustering |
metaClusters, metaAssign |
Meta-Clustering for defining isomorphisms on cells across clusters. |
| MMClustering |
1.0 |
fcsFiles |
clusters, postProb, report, mmSpecs, mmParams |
Normal, t, Skew-normal, and skew-t Mixture-Model Clustering. |
| OptimalClustering |
1.0 |
clusters, clustStat |
clusters, report |
The component takes the output of the MMClustering component,
where each data sample has been clustered with multiple different cluster
numbers, and determines the optimal cluster number for each sample. |
| PairWiseClusterPlot |
1.0 |
clusterFiles, clusters, filteredFiles, filtered |
report |
Produces pairwise scatter plots from clustered and filtered data. |
| PlotChannels |
1.0 |
in, fs |
out |
Component meant to visualize Flow and Mass Cytometry data before and after transformations. |
| SamSpectral |
1.1 |
list, in |
clusters, out |
SamSPECTRAL clustering of flow cytometry data as described by Zare et al (2010). |
| Summarise |
1.0 |
clusterFiles, reference |
summaries |
Summarises values for different rows of a file (i.e. reference) according to the clustered
and possibly filtered result of the file (i.e. clusterFiles). |
| Transformation |
1.0 |
in |
out |
Cell fluorescense intensity transformation for FACS data. |
Up: Category summary
FlowCytometry