Package: uSORT 1.33.0

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_1.33.0.tar.gz

uSORT_1.33.0.tar.gz(r-4.5-noble)uSORT_1.33.0.tar.gz(r-4.4-noble)
uSORT_1.33.0.tgz(r-4.4-emscripten)uSORT_1.33.0.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'))

On BioConductor:uSORT-1.33.0(bioc 3.21)uSORT-1.32.0(bioc 3.20)

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

immunooncology rnaseq gui cellbiology dnaseq

3.30 score 222 downloads 15 exports 85 dependencies

Last updated 2 months agofrom:9c366f247f. Checks:OK: 1 WARNING: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 18 2024
R-4.5-linux	WARNING	Dec 18 2024

Exports:autoSPIN driving_force_gene_selection elbow_detection monocle_wrapper neighborhood_sortingcost pca_gene_selection Rwanderlust SPIN STS_sortingcost sWanderlust uSORT uSORT_GUI uSORT_preProcess uSORT_sorting_wrapper uSORT_write_results

Dependencies:BH Biobase BiocGenerics BiocManager biocViews bitops caTools class cli cluster colorspace combinat cpp11 DDRTree DEoptimR diptest dplyr fansi farver fastICA flexmix fpc generics ggplot2 glue gplots graph gridExtra gtable gtools HSMMSingleCell igraph irlba isoband kernlab KernSmooth labeling lattice leidenbase lifecycle limma magrittr MASS Matrix matrixStats mclust mgcv modeltools monocle munsell nlme nnet pheatmap pillar pkgconfig plyr prabclus proxy R6 RANN RBGL RColorBrewer Rcpp RcppEigen RCurl reshape2 rlang robustbase RSpectra Rtsne RUnit scales slam statmod stringi stringr tibble tidyselect utf8 vctrs VGAM viridis viridisLite withr XML

uSORT: Quick Start

Rendered fromuSORT_quick_start.Rmdusingknitr::rmarkdownon Dec 18 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A wrapper function for autoSPIN sorting method	autoSPIN
A modified monocle's function	clusterGenes1
A modified monocle's function	compareModels1
A modified monocle's helper function	diff_test_helper1
differential gene test	differentialGeneTest1
A distance function A distance function computes cell-to-cell distance matrix.	distance.function
A feature/ gene selection function	driving_force_gene_selection
A elbow detection function	elbow_detection
A function for constructing a Monocle's CellDataSet object from an expression matrix	EXP_to_CellDataSet
A gene detection function	fluidigmSC_analyzeGeneDetection
An outlier detection function	fluidigmSC_identifyExpOutliers
A gene finding function	fluidigmSC_isElementIgnoreCase
An expression reading function	fluidigmSC_readLinearExp
A gene trimming function	fluidigmSC_removeGenesByLinearExpForAllType
A gene trimming function	fluidigmSC_removeGenesByLinearExpForAllType_log2
A wrapper function for Monocle sorting method	monocle_wrapper
A sorting function using the Neighborhood algorithm	neighborhood_sorting
A wrapper function for Neighborhood sorting.	neighborhood_sorting_wrapper
A cost computation function for Neighborhood algorithm	neighborhood_sortingcost
Gene selection using PCA technique	pca_gene_selection
R inplementation of wanderlust	Rwanderlust
An expression scattering measurement function	scattering_quantification_per_gene
GUI for sorting method paramters	sorting_method_parameter_GUI
A wrapper function for SPIN sorting method	SPIN
A sorting function using the Side-to-Side (STS) algorithm	STS_sorting
A wrapper function for Side-to-Side (STS) sorting.	STS_sorting_wrapper
A cost computation function for Side-to-Side (STS) algorithm	STS_sortingcost
A summed local variance function	summed_local_variance
A summed local variance function for cyclical linear data type	summed_local_variance_cyclical
A summed local variance function for strictly linear data type	summed_local_variance_linear
sWanderlust	sWanderlust
determining initial trajectory and landmarks	trajectory_landmarks
uSORT: A self-refining ordering pipeline for gene selection	uSORT-package uSORT
The user friendly GUI for 'uSORT-package'	uSORT_GUI
The GUI for inputting paramters for uSORT	uSORT_parameters_GUI
A data loading and pre-processing function	uSORT_preProcess
wrapper of all avaliable sorting methods in uSORT	uSORT_sorting_wrapper
Resluts parsing for uSORT	uSORT_write_results
A utility function for scattering_quantification_per_gene	variability_per_gene
a wrapper of wanderlust for sWanderlust	wanderlust_wrapper