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

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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... 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 north node in virgo 5th house

SONGDONGYUAN1994/PseudotimeDE: README.md

WebSep 29, 2024 · runPseudotimeDE: Perform Differential Expression Test on a List of … 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 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 how to schedule 10 hour shifts