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 WebApr 29, 2024 · PseudotimeDE: inference of differential gene expression along cell …
PseudotimeDE: inference of differential gene expression along cell …
WebSep 29, 2024 · GitHub SONGDONGYUAN1994/PseudotimeDE: Inference of differential … WebNational Center for Biotechnology Information procheck oee login
PseudotimeDE: inference of differential gene expression along cell …
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 WebMar 27, 2024 · PseudotimeDE is flexible in allowing users to specify the pseudotime … 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 … rehobot bushing tool