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| AddTsne | Add tSNE to your results. |
| bz.gmcsf.final | Bodenmiller-Zunder GM-CSF post-SCONE final data |
| bz.gmcsf.final.norm.scale | Bodenmiller-Zunder GM-CSF post-SCONE final data, that's been quantile normalized and z scored. |
| exist | Random musing |
| FcsToTibble | Takes a file as input and returns a data frame of cells by features |
| Fnn | Compute knn using the fnn algorithm |
| funct.markers | Functional markers from the Wanderlust dataset. |
| GetKnnDe | Get the KNN density estimaion |
| GetMarkerNames | Takes in an example file as input and returns all marker names |
| Impute | Imputes values for all markers (used as input) for each cell |
| ImputeTesting | Impute testing |
| input.markers | Input markers for the Wanderlust dataset |
| LogTransformQ | Log transform the q values |
| MakeHist | make.hist |
| MakeKnnList | Make list of cells by features for each KNN member |
| markers | Markers for the Wanderlust dataset |
| MeaningOfLife | Meaning of life |
| MultipleDonorStatistics | Runs a t test on the medians or means of multiple donors for the same condition |
| ParseMarkers | Parse markers contained in a Sconify-directed marker file |
| PostProcessing | Post-processing for scone analysks. |
| ProcessMultipleFiles | Converts multiple files into a concatenated data frame |
| QCorrectionThresholding | Corrects all p values for multiple hypotheses, sets threshold for which change values should be reported |
| QuantNormalize | Performs quantile normalization on the data frame (patient) of interest |
| QuantNormalizeElements | Takes a list of tibbles as input, and performs per-column quantile normalization, then outputs the quantile normalized list |
| RunStatistics | Performs a series of statistical tests on the batch of cells of interest. |
| SconeValues | Master function for per-knn statistics functionality, integrating the other non-exported functions within this script. |
| SplitFile | Runs "process.multiple.files" on a single file, splits it randomly, and presends half of it is "unstim" and half of it is "stim" |
| StringToNumbers | Transform strings to numbers. |
| SubsampleAndTsne | Subsample data and run tSNE |
| TsneVis | Plot a tSNE map colored by a marker of interest |
| wand.combined | Wanderlust data combined basal and IL7 cells |
| wand.final | Post-scone output of the "combiend" Wanderlust data. |
| wand.ideal.k | A named vector to help the user determine the ideal k for the Wanderlust dataset. |
| wand.il7 | Wanderlust IL7 data |
| wand.scone | Wanderlust scone output |