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.

Author
Mai Chan Lau, Hao Chen, Jinmiao Chen
Date of publication
None
Maintainer
Hao Chen <chen_hao@immunol.a-star.edu.sg>
License
Artistic-2.0
Version
1.0.0

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

Files in this package

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