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 |