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

This package is designed to uncover the intrinsic cell progression path from single-cell RNA-seq data. It incorporates data pre-processing, preliminary PCA gene selection, preliminary cell ordering, feature selection, refined cell ordering, and post-analysis interpretation and visualization.

AuthorMai Chan Lau, Hao Chen, Jinmiao Chen
Date of publicationNone
MaintainerHao Chen <chen_hao@immunol.a-star.edu.sg>
LicenseArtistic-2.0
Version1.0.0

View on Bioconductor

Man pages

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...

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...

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...

summed_local_variance_linear: A summed local variance function for strictly linear data...

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

Functions

autoSPIN Man page
clusterGenes1 Man page
compareModels1 Man page
differentialGeneTest1 Man page
diff_test_helper1 Man page
distance.function Man page
driving_force_gene_selection Man page
elbow_detection Man page
EXP_to_CellDataSet Man page
fluidigmSC_analyzeGeneDetection Man page
fluidigmSC_identifyExpOutliers Man page
fluidigmSC_isElementIgnoreCase Man page
fluidigmSC_readLinearExp Man page
fluidigmSC_removeGenesByLinearExpForAllType Man page
fluidigmSC_removeGenesByLinearExpForAllType_log2 Man page
monocle_wrapper Man page
neighborhood_sorting Man page
neighborhood_sortingcost Man page
neighborhood_sorting_wrapper Man page
pca_gene_selection Man page
Rwanderlust Man page
scattering_quantification_per_gene Man page
sorting_method_parameter_GUI Man page
SPIN Man page
STS_sorting Man page
STS_sortingcost Man page
STS_sorting_wrapper Man page
summed_local_variance Man page
summed_local_variance_cyclical Man page
summed_local_variance_linear Man page
sWanderlust Man page
trajectory_landmarks Man page
uSORT Man page
uSORT_GUI Man page
uSORT-package Man page
uSORT_parameters_GUI Man page
uSORT_preProcess Man page
uSORT_sorting_wrapper Man page
uSORT_write_results Man page
variability_per_gene Man page
wanderlust_wrapper Man page

Files

uSORT/DESCRIPTION
uSORT/NAMESPACE
uSORT/R
uSORT/R/SPIN.r
uSORT/R/Swanderlust.R
uSORT/R/autoSPIN.r
uSORT/R/monocle.R uSORT/R/uSORT_GUI.R uSORT/R/uSORT_GeneSelection.R uSORT/R/uSORT_main.R uSORT/R/uSORT_postProcess.R uSORT/R/uSort_preProcess.R uSORT/R/uSort_sorting_wrapper.R
uSORT/build
uSORT/build/vignette.rds
uSORT/inst
uSORT/inst/NEWS.Rd
uSORT/inst/doc
uSORT/inst/doc/uSORT_quick_start.R
uSORT/inst/doc/uSORT_quick_start.Rmd
uSORT/inst/doc/uSORT_quick_start.html
uSORT/inst/extdata
uSORT/inst/extdata/TPM_test.txt
uSORT/inst/unitTests
uSORT/inst/unitTests/test_Rwanderlust.R
uSORT/man
uSORT/man/EXP_to_CellDataSet.Rd uSORT/man/Rwanderlust.Rd uSORT/man/SPIN.Rd uSORT/man/STS_sorting.Rd uSORT/man/STS_sorting_wrapper.Rd uSORT/man/STS_sortingcost.Rd uSORT/man/autoSPIN.Rd uSORT/man/clusterGenes1.Rd uSORT/man/compareModels1.Rd uSORT/man/diff_test_helper1.Rd uSORT/man/differentialGeneTest1.Rd uSORT/man/distance.function.Rd uSORT/man/driving_force_gene_selection.Rd uSORT/man/elbow_detection.Rd uSORT/man/fluidigmSC_analyzeGeneDetection.Rd uSORT/man/fluidigmSC_identifyExpOutliers.Rd uSORT/man/fluidigmSC_isElementIgnoreCase.Rd uSORT/man/fluidigmSC_readLinearExp.Rd uSORT/man/fluidigmSC_removeGenesByLinearExpForAllType.Rd uSORT/man/fluidigmSC_removeGenesByLinearExpForAllType_log2.Rd uSORT/man/monocle_wrapper.Rd uSORT/man/neighborhood_sorting.Rd uSORT/man/neighborhood_sorting_wrapper.Rd uSORT/man/neighborhood_sortingcost.Rd uSORT/man/pca_gene_selection.Rd uSORT/man/sWanderlust.Rd uSORT/man/scattering_quantification_per_gene.Rd uSORT/man/sorting_method_parameter_GUI.Rd uSORT/man/summed_local_variance.Rd uSORT/man/summed_local_variance_cyclical.Rd uSORT/man/summed_local_variance_linear.Rd uSORT/man/trajectory_landmarks.Rd uSORT/man/uSORT.Rd uSORT/man/uSORT_GUI.Rd uSORT/man/uSORT_parameters_GUI.Rd uSORT/man/uSORT_preProcess.Rd uSORT/man/uSORT_sorting_wrapper.Rd uSORT/man/uSORT_write_results.Rd uSORT/man/variability_per_gene.Rd uSORT/man/wanderlust_wrapper.Rd
uSORT/tests
uSORT/tests/runTests.R
uSORT/vignettes
uSORT/vignettes/driver_gene_profile.png
uSORT/vignettes/preliminary_sort_distance.png
uSORT/vignettes/preliminary_sorting_cell_type.png
uSORT/vignettes/refined_sort_distance.png
uSORT/vignettes/refined_sorting_cell_type.png
uSORT/vignettes/uSORT_GUI.png
uSORT/vignettes/uSORT_para_GUI.png
uSORT/vignettes/uSORT_quick_start.Rmd
uSORT/vignettes/uSORT_workflow.png

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