2024 Pseudotimede github

Pseudotimede github

Author: nuxu

August undefined, 2024

WebThe pseudotimeDE R package (Song and others, 2024) does allow for an arbitrary pseudotime estimation technique, but it fits negative binomial generalized additive models (GAMs) by default, and... WebSep 29, 2024 · runPseudotimeDE: Perform Differential Expression Test on a List of …

PseudotimeDE: inference of differential gene expression

WebJun 10, 2024 · LPS_ori_tbl: A tibble containing the inferred pseudotime of 'LPS_sce' by... LPS_sce: A SingelCellExperiment dataset containing 4,016 genes and 390... LPS_sub_tbl: A list of tibbles containing the inferred pseudotime of each... plotCurve: Plot the Fitted Model (Gene Trajectory) plotUncertainty: Plot the Pseudotime of Subsamples pseudotimeDE: … WebSep 29, 2024 · GitHub SONGDONGYUAN1994/PseudotimeDE: Inference of differential … citizen men\u0027s bx1000-57e world time perpetual

pseudotime · GitHub Topics · GitHub

WebPseudotime is a measure of how much progress an individual cell has made through a process such as cell differentiation. In many biological processes, cells do not progress in perfect synchrony. In single-cell expression studies of processes such as cell differentiation, captured cells might be widely distributed in terms of progress. WebJun 20, 2024 · GitHub is where people build software. More than 94 million people use … WebNov 18, 2024 · Comprehensive simulations and real-data applications verify that PseudotimeDE provides well-calibrated p -values essential for controlling FDR and downstream analysis and that PseudotimeDE is... dichromat mit ethanol

SONGDONGYUAN1994/PseudotimeDE source listing

http://jsb.ucla.edu/sites/default/files/news/PseudotimeDE_poster.pdf WebSep 29, 2024 · Given a single cell RNA-seq data and a pseudotime inference method, pseudotimeDE returns the p-value of each gene. SONGDONGYUAN1994/PseudotimeDE: Inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data version 1.0.0 from GitHub citizen men\u0027s brown leather strap watchPseudotimeDE is developed to perfrom the differential expression (DE) test on genes along pseudotime (trajectory). Users can choose the pseudotime inference methods based on their preference. Basically, PseudotimeDE will use subsampling to capture the uncertainty of inferred pseudotime, and generate well … See more 2024/12/02:Update the vignettes 2024/11/12:Replaced parallel.mclapply by BiocParallel.bplapply 2024/11/3:Added QGAM(Smooth additive quantile regression model) as a model option. 2024/10/25:Added … See more The package is not on Bioconductor or CRAN yet. For installation please use the following codes in R. Please note that PseudotimeDEcan be computationally intensive; we … See more PseudotimeDE assumes that the latent pseudotime does exist and your pseudotime inference method can somehow capture it. If there is no latent pseudotime at all (e.g., the data is many iid random Poisson … See more For usage, please check the vignettes. A separate vignettes(QGAM)is created for PseudoimeDE when its model parameter is set as 'qgam'. If you meet problems, please contact [email protected]. See more dichromat photography

"WebLPS_ori_tbl: A tibble containing the inferred pseudotime of 'LPS_sce' by... LPS_sce: A SingelCellExperiment dataset containing 4,016 genes and 390... LPS_sub_tbl: A list of tibbles containing the inferred pseudotime of each... plotCurve: Plot the Fitted Model (Gene Trajectory) plotUncertainty: Plot the Pseudotime of Subsamples pseudotimeDE: Perform … " - Pseudotimede github

Pseudotimede github

Molecular estimation of neurodegeneration pseudotime in older

WebR code for temporal phenotyping via Topological Data Analysis and Pseudo Time - GitHub … WebGitHub SONGDONGYUAN1994/PseudotimeDE R/PseudotimeDE.R R/PseudotimeDE.R In SONGDONGYUAN1994/PseudotimeDE: Inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data Defines functions zinbgamdzinb.logfit_gamfit_qgampseudotimeDE Documented in

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WebMar 27, 2024 · PseudotimeDE is flexible in allowing users to specify the pseudotime … WebPseudotimeDE. PseudotimeDE is a robust method that accounts for the uncertainty in pseudotime inference and thus identifies DE genes along cell pseudotime with well-calibrated p-values. PseudotimeDE is flexible in allowing users to specify the pseudotime inference method and to choose the appropriate model for scRNA-seq data. Latest News

WebFor Slc39a10, both PseudotimeDE and Monocle3-DE yield small p-values (p < 1e − 6), while tradeSeq does not (p > 0.1). For Sst, PseudotimeDE yields larger p-values than tradeSeq and Monocle3-DE do. WebOct 1, 2016 · Motivation: Repeated cross-sectional time series single cell data confound …

WebApr 6, 2024 · PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data Dongyuan Song ; Jingyi Jessica Li Analysis code and preprocessed datasets for the paper. WebWe proposed PseudotimeDE, a differentially expressed (DE) gene identification method that adapts to various pseudotime inference methods, accounts for pseudotime inference uncertainty, and outputs well-calibrated p-values. Learn more in …

WebApr 29, 2024 · PseudotimeDE outperforms four state-of-the-art methods (tradeSeq, …

WebApr 22, 2024 · Here we propose PseudotimeDE, a DE gene identification method that … dichromatlösung formelWebMar 27, 2024 · PseudotimeDE is flexible in allowing users to specify the pseudotime inference method and to choose the appropriate model for scRNA-seq data. Comprehensive simulations and real-data applications verify that PseudotimeDE provides well-calibrated p -values essential for controlling FDR and downstream analysis and that PseudotimeDE is … citizen men\u0027s dress watchesWebApr 29, 2024 · PseudotimeDE: inference of differential gene expression along cell … citizen men\u0027s eco day \u0026 date cream dial watchWebNov 18, 2024 · PseudotimeDE is flexible in allowing users to specify the pseudotime inference method and to choose the appropriate model for scRNA-seq data. Comprehensive simulations and real-data applications verify that PseudotimeDE provides well-calibrated p -values essential for controlling FDR and downstream analysis and that PseudotimeDE is … citizen men\u0027s eco-drive leather strap watchWebApr 29, 2024 · PseudotimeDE yields the FDP closest to 0.05. d, i ROC curves and AUROC values of the five DE methods. PseudotimeDE achieves the highest AUROC. e, j Power of the five DE methods under the FDP = 0. ... citizen men\u0027s eco-drive pcat watchWebNov 17, 2024 · Finally, PseudotimeDE calculates a right-tail p-value for the gene from the gene’s test statistic in the original dataset and the approximate null distribution. Further detail of PseudotimeDE is described in Methods. Simulations verify that pseudotimeDE outperforms existing methods in the validity of p-values and the identiﬁcation power. dichromat mit wasserstoffperoxidWebApr 29, 2024 · Here we propose PseudotimeDE, a DE gene identification method that adapts to various pseudotime inference methods, accounts for pseudotime inference uncertainty, and outputs well-calibrated p-values. Comprehensive simulations and real-data applications verify that PseudotimeDE outperforms existing methods in false discovery rate control … citizen men\u0027s diamond watch