uSORT: A self-refining ordering pipeline for gene selection

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Documentation for package ‘uSORT’ version 1.35.0

• 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