LineagePulse
Differential expression analysis and model fitting for single-cell RNA-seq data
Bioconductor version: Release (3.17)
LineagePulse is a differential expression and expression model fitting package tailored to single-cell RNA-seq data (scRNA-seq). LineagePulse accounts for batch effects, drop-out and variable sequencing depth. One can use LineagePulse to perform longitudinal differential expression analysis across pseudotime as a continuous coordinate or between discrete groups of cells (e.g. pre-defined clusters or experimental conditions). Expression model fits can be directly extracted from LineagePulse.
Author: David S Fischer [aut, cre], Fabian Theis [ctb], Nir Yosef [ctb]
Maintainer: David S Fischer <david.fischer at helmholtz-muenchen.de>
citation("LineagePulse")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("LineagePulse")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("LineagePulse")| LineagePulse | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, CellBiology, DifferentialExpression, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, TimeCourse |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (5.5 years) |
| License | Artistic-2.0 |
| Depends | |
| Imports | BiocParallel, circlize, compiler, ComplexHeatmap, ggplot2, gplots, grDevices, grid, knitr, Matrix, methods, RColorBrewer, SingleCellExperiment, splines, stats, SummarizedExperiment, utils |
| Linking To | |
| Suggests | |
| System Requirements | |
| Enhances | |
| URL | |
| Bug Reports | https://github.com/YosefLab/LineagePulse/issues |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | LineagePulse_1.20.0.tar.gz |
| Windows Binary | LineagePulse_1.20.0.zip |
| macOS Binary (x86_64) | LineagePulse_1.20.0.tgz |
| macOS Binary (arm64) | LineagePulse_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/LineagePulse |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/LineagePulse |
| Bioc Package Browser | https://code.bioconductor.org/browse/LineagePulse/ |
| Package Short Url | https://bioconductor.org/packages/LineagePulse/ |
| Package Downloads Report | Download Stats |