Man pages for cjscholz/ClEvaR
Cluster Evaluation in R
| AMI | Adjusted Mutual Information |
| characterizeMarkerThresholds | Characterize Marker Thresholds |
| clusterExprsSummaryMatrix | Construct a matrix of expression summary values per cluster. |
| clusterGranularity | Cluster Granularity |
| clusterIntegrity | Cluster Integrity |
| confusionHeatmap | Plot a confusion heatmap. |
| EMI | Expected Mutual Information |
| entropy | Calculate Shannon Entropy |
| findMarkerThresholds | Find Marker Thresholds |
| HBITM | Compute the HBITM similarity between two clusterings. |
| immune_markers_blueprint | Cell type marker genes and scores. |
| immune_markers_canonical | Canonical marker genes of the hematopoietic lineage. |
| immune_markers_lm22 | Immune cell marker genes and scores. |
| immune_markers_novershtern2011 | Marker genes of various immune cell types. |
| integrityPlot | Generate cluster integrity plot. |
| makeDonuts | Make Donut Plot. |
| makeScatterplot | Make a scatterplot. |
| maxChunkFGH5 | Determine the number of chunks of a FASTGenomics Matrix HDF5... |
| MI | Mutual Information |
| multiplot | Multiple Plot Function |
| NMI | Normalized Mutual Information |
| observationsFGH5 | Retrieve observations from FASTGenomics Matrix HDF5 file. |
| plotDonuts | Plot donuts. |
| plotLegend | Plot the legend(s) for donut plots. |
| readAEoutput | Read FASTGenomics Autoencoder Output |
| readFGH5 | Read FASTGenomics Matrix in HDF5 format. |
| readFGH5dense | Read FASTGenomics Matrix in dense HDF5 format. |
| readFGH5sparse | Read FASTGenomics Matrix in sparse HDF5 format. |
| scale_01 | Scale to 0 - 1 range |
| scoreCells | Classify cells using marker genes. |
| scoreCellsInChunks | Classify cells using marker genes. |
| selectMarkerGenes | Select Marker Genes |
| variablesFGH5 | Retrieve variables from FASTGenomics Matrix HDF5 file. |
| zeisel2018 | Molecular architecture of the mouse nervous system. |
