Package: uSORT 1.31.0

Hao Chen

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.

Authors:Mai Chan Lau, Hao Chen, Jinmiao Chen

uSORT_1.31.0.tar.gz


uSORT_1.31.0.tar.gz(r-4.5-noble)uSORT_1.31.0.tar.gz(r-4.4-noble)
uSORT_1.31.0.tgz(r-4.4-emscripten)uSORT_1.31.0.tgz(r-4.3-emscripten)
uSORT.pdf |uSORT.html✨
uSORT/json (API)
NEWS

# Install 'uSORT' in R:
install.packages('uSORT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:uSORT-1.31.0(bioc 3.20)uSORT-1.30.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

15 exports 0.71 score 85 dependencies

Last updated 2 months agofrom:dbd8244b45

Exports:autoSPINdriving_force_gene_selectionelbow_detectionmonocle_wrapperneighborhood_sortingcostpca_gene_selectionRwanderlustSPINSTS_sortingcostsWanderlustuSORTuSORT_GUIuSORT_preProcessuSORT_sorting_wrapperuSORT_write_results

Dependencies:BHBiobaseBiocGenericsBiocManagerbiocViewsbitopscaToolsclasscliclustercolorspacecombinatcpp11DDRTreeDEoptimRdiptestdplyrfansifarverfastICAflexmixfpcgenericsggplot2gluegplotsgraphgridExtragtablegtoolsHSMMSingleCelligraphirlbaisobandkernlabKernSmoothlabelinglatticeleidenbaselifecyclelimmamagrittrMASSMatrixmatrixStatsmclustmgcvmodeltoolsmonoclemunsellnlmennetpheatmappillarpkgconfigplyrprabclusproxyR6RANNRBGLRColorBrewerRcppRcppEigenRCurlreshape2rlangrobustbaseRSpectraRtsneRUnitscalesslamstatmodstringistringrtibbletidyselectutf8vctrsVGAMviridisviridisLitewithrXML

uSORT: Quick Start

Rendered fromuSORT_quick_start.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2016-10-02
Started: 2016-10-02

Readme and manuals

Help Manual

Help pageTopics
A wrapper function for autoSPIN sorting methodautoSPIN
A modified monocle's functionclusterGenes1
A modified monocle's functioncompareModels1
A modified monocle's helper functiondiff_test_helper1
differential gene testdifferentialGeneTest1
A distance function A distance function computes cell-to-cell distance matrix.distance.function
A feature/ gene selection functiondriving_force_gene_selection
A elbow detection functionelbow_detection
A function for constructing a Monocle's CellDataSet object from an expression matrixEXP_to_CellDataSet
A gene detection functionfluidigmSC_analyzeGeneDetection
An outlier detection functionfluidigmSC_identifyExpOutliers
A gene finding functionfluidigmSC_isElementIgnoreCase
An expression reading functionfluidigmSC_readLinearExp
A gene trimming functionfluidigmSC_removeGenesByLinearExpForAllType
A gene trimming functionfluidigmSC_removeGenesByLinearExpForAllType_log2
A wrapper function for Monocle sorting methodmonocle_wrapper
A sorting function using the Neighborhood algorithmneighborhood_sorting
A wrapper function for Neighborhood sorting.neighborhood_sorting_wrapper
A cost computation function for Neighborhood algorithmneighborhood_sortingcost
Gene selection using PCA techniquepca_gene_selection
R inplementation of wanderlustRwanderlust
An expression scattering measurement functionscattering_quantification_per_gene
GUI for sorting method paramterssorting_method_parameter_GUI
A wrapper function for SPIN sorting methodSPIN
A sorting function using the Side-to-Side (STS) algorithmSTS_sorting
A wrapper function for Side-to-Side (STS) sorting.STS_sorting_wrapper
A cost computation function for Side-to-Side (STS) algorithmSTS_sortingcost
A summed local variance functionsummed_local_variance
A summed local variance function for cyclical linear data typesummed_local_variance_cyclical
A summed local variance function for strictly linear data typesummed_local_variance_linear
sWanderlustsWanderlust
determining initial trajectory and landmarkstrajectory_landmarks
uSORT: A self-refining ordering pipeline for gene selectionuSORT-package uSORT
The user friendly GUI for 'uSORT-package'uSORT_GUI
The GUI for inputting paramters for uSORTuSORT_parameters_GUI
A data loading and pre-processing functionuSORT_preProcess
wrapper of all avaliable sorting methods in uSORTuSORT_sorting_wrapper
Resluts parsing for uSORTuSORT_write_results
A utility function for scattering_quantification_per_genevariability_per_gene
a wrapper of wanderlust for sWanderlustwanderlust_wrapper