目录
- Ralso ignore NA in ll in drop-out test8年前
- instAdded negative binomial noise model fitting as reference into core in same code structure as ZINBs. Preparing switch of lsModels to classes for those models. Upadated intilisation of impulse model. Changed default of LP main to splines.8年前
- manReduced content in man page of runLineagePulse and referred to vignette to not have text double.8年前
- vignettesMoved some package imports to suggests8年前
- DESCRIPTIONAdded ImmunoOncology biocView into DESCRIPTION7年前
- NAMESPACEupdated namespace8年前
- README.mdFinal commit before RSA is branched out. LP is functional as a package.8年前
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LineagePulse
Differential expression analysis and model fitting for single-cell RNA-seq data in pseudotime
LineagePulse is a differential expression algorithm for single-cell RNA-seq (scRNA-seq) data. Its main application is differential expression analysis across pseudotemporal orderings (developmental trajectories) of scRNA-seq data. LineagePulse can also be used for group-wise differential expression tests. As LineagePulse is based on model fitting, it can also be used for batch correction and gene expression trajectory estimation only.
INSTALLATION
Clone the GitHub LineagePulse repository first into you local target directory and then install the package via “R CMD INSTALL .”.
VIGNETTE
View the vignette (.html) in your browser by double clicking on “vignettes/LineagePulse_Tutorial.Rmd”.
Problems with BiocParallel:
LineagePulse is parallelised with BiocParallel. If BiocParallel does not start any processes during the model estimation, add options(bphost=”localhost”) into your R script before the first call to any LineagePulse function.