uSORT: uSORT: A self-refining ordering pipeline for gene selection
Version 1.2.0

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
Bioconductor views CellBiology DNASeq GUI RNASeq
Date of publicationNone
MaintainerHao Chen <chen_hao@immunol.a-star.edu.sg>
LicenseArtistic-2.0
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("uSORT")

Getting started

uSORT: Quick Start

Popular man pages

autoSPIN: A wrapper function for autoSPIN sorting method
elbow_detection: A elbow detection function
EXP_to_CellDataSet: A function for constructing a Monocle's CellDataSet object...
Rwanderlust: R inplementation of wanderlust
STS_sorting: A sorting function using the Side-to-Side (STS) algorithm
uSORT_write_results: Resluts parsing for uSORT
wanderlust_wrapper: a wrapper of wanderlust for sWanderlust
See all...

All man pages Function index File listing

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

Files

DESCRIPTION
NAMESPACE
R
R/SPIN.r
R/Swanderlust.R
R/autoSPIN.r
R/monocle.R
R/uSORT_GUI.R
R/uSORT_GeneSelection.R
R/uSORT_main.R
R/uSORT_postProcess.R
R/uSort_preProcess.R
R/uSort_sorting_wrapper.R
build
build/vignette.rds
inst
inst/NEWS.Rd
inst/doc
inst/doc/uSORT_quick_start.R
inst/doc/uSORT_quick_start.Rmd
inst/doc/uSORT_quick_start.html
inst/extdata
inst/extdata/TPM_test.txt
inst/unitTests
inst/unitTests/test_Rwanderlust.R
man
man/EXP_to_CellDataSet.Rd
man/Rwanderlust.Rd
man/SPIN.Rd
man/STS_sorting.Rd
man/STS_sorting_wrapper.Rd
man/STS_sortingcost.Rd
man/autoSPIN.Rd
man/clusterGenes1.Rd
man/compareModels1.Rd
man/diff_test_helper1.Rd
man/differentialGeneTest1.Rd
man/distance.function.Rd
man/driving_force_gene_selection.Rd
man/elbow_detection.Rd
man/fluidigmSC_analyzeGeneDetection.Rd
man/fluidigmSC_identifyExpOutliers.Rd
man/fluidigmSC_isElementIgnoreCase.Rd
man/fluidigmSC_readLinearExp.Rd
man/fluidigmSC_removeGenesByLinearExpForAllType.Rd
man/fluidigmSC_removeGenesByLinearExpForAllType_log2.Rd
man/monocle_wrapper.Rd
man/neighborhood_sorting.Rd
man/neighborhood_sorting_wrapper.Rd
man/neighborhood_sortingcost.Rd
man/pca_gene_selection.Rd
man/sWanderlust.Rd
man/scattering_quantification_per_gene.Rd
man/sorting_method_parameter_GUI.Rd
man/summed_local_variance.Rd
man/summed_local_variance_cyclical.Rd
man/summed_local_variance_linear.Rd
man/trajectory_landmarks.Rd
man/uSORT.Rd
man/uSORT_GUI.Rd
man/uSORT_parameters_GUI.Rd
man/uSORT_preProcess.Rd
man/uSORT_sorting_wrapper.Rd
man/uSORT_write_results.Rd
man/variability_per_gene.Rd
man/wanderlust_wrapper.Rd
tests
tests/runTests.R
vignettes
vignettes/driver_gene_profile.png
vignettes/preliminary_sort_distance.png
vignettes/preliminary_sorting_cell_type.png
vignettes/refined_sort_distance.png
vignettes/refined_sorting_cell_type.png
vignettes/uSORT_GUI.png
vignettes/uSORT_para_GUI.png
vignettes/uSORT_quick_start.Rmd
vignettes/uSORT_workflow.png
uSORT documentation built on May 20, 2017, 9:46 p.m.

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