# uSORT: A self-refining ordering pipeline for gene selection

## Documentation for package ‘uSORT’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

uSORT-package | uSORT: A self-refining ordering pipeline for gene selection
autoSPIN | A wrapper function for autoSPIN sorting method
clusterGenes1 | A modified monocle's function
compareModels1 | A modified monocle's function
differentialGeneTest1 | differential gene test
diff_test_helper1 | A modified monocle's helper function
distance.function | A distance function A distance function computes cell-to-cell distance matrix.
driving_force_gene_selection | A feature/ gene selection function
elbow_detection | A elbow detection function
EXP_to_CellDataSet | A function for constructing a Monocle's CellDataSet object from an expression matrix
fluidigmSC_analyzeGeneDetection | A gene detection function
fluidigmSC_identifyExpOutliers | An outlier detection function
fluidigmSC_isElementIgnoreCase | A gene finding function
fluidigmSC_readLinearExp | An expression reading function
fluidigmSC_removeGenesByLinearExpForAllType | A gene trimming function
fluidigmSC_removeGenesByLinearExpForAllType_log2 | A gene trimming function
monocle_wrapper | A wrapper function for Monocle sorting method
neighborhood_sorting | A sorting function using the Neighborhood algorithm
neighborhood_sortingcost | A cost computation function for Neighborhood algorithm
neighborhood_sorting_wrapper | A wrapper function for Neighborhood sorting.
pca_gene_selection | Gene selection using PCA technique
Rwanderlust | R inplementation of wanderlust
scattering_quantification_per_gene | An expression scattering measurement function
sorting_method_parameter_GUI | GUI for sorting method paramters
SPIN | A wrapper function for SPIN sorting method
STS_sorting | A sorting function using the Side-to-Side (STS) algorithm
STS_sortingcost | A cost computation function for Side-to-Side (STS) algorithm
STS_sorting_wrapper | A wrapper function for Side-to-Side (STS) sorting.
summed_local_variance | A summed local variance function
summed_local_variance_cyclical | A summed local variance function for cyclical linear data type
summed_local_variance_linear | A summed local variance function for strictly linear data type
sWanderlust | sWanderlust
trajectory_landmarks | determining initial trajectory and landmarks
uSORT | uSORT: A self-refining ordering pipeline for gene selection
uSORT_GUI | The user friendly GUI for 'uSORT-package'
uSORT_parameters_GUI | The GUI for inputting paramters for uSORT
uSORT_preProcess | A data loading and pre-processing function
uSORT_sorting_wrapper | wrapper of all avaliable sorting methods in uSORT
uSORT_write_results | Resluts parsing for uSORT
variability_per_gene | A utility function for scattering_quantification_per_gene
wanderlust_wrapper | a wrapper of wanderlust for sWanderlust