scLANE
This is the released version of scLANE; for the devel version, see scLANE.
Model Gene Expression Dynamics with Spline-Based NB GLMs, GEEs, & GLMMs
Bioconductor version: Release (3.22)
Our scLANE model uses truncated power basis spline models to build flexible, interpretable models of single cell gene expression over pseudotime or latent time. The modeling architectures currently supported are Negative-binomial GLMs, GEEs, & GLMMs. Downstream analysis functionalities include model comparison, dynamic gene clustering, smoothed counts generation, gene set enrichment testing, & visualization.
Author: Jack R. Leary [aut, cre]
, Rhonda Bacher [ctb, fnd]
Maintainer: Jack R. Leary <j.leary at ufl.edu>
citation("scLANE")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scLANE")
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("scLANE")| Interpretable Trajectory DE Testing | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, DifferentialExpression, GeneExpression, GeneSetEnrichment, RNASeq, Regression, Sequencing, SingleCell, Software, TimeCourse, Transcriptomics, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | glm2, magrittr, R (>= 4.5.0) |
| Imports | geeM, MASS, mpath, dplyr, stats, utils, withr, purrr, tidyr, furrr, doSNOW, gamlss, scales, future, Matrix, ggplot2, splines, foreach, glmmTMB, parallel, RcppEigen, bigstatsr, tidyselect, broom.mixed, Rcpp |
| System Requirements | |
| URL | https://github.com/jr-leary7/scLANE |
| Bug Reports | https://github.com/jr-leary7/scLANE/issues |
See More
| Suggests | covr, grid, coop, uwot, scran, ggh4x, knitr, UCell, irlba, rlang, magick, igraph, scater, gtable, ggpubr, viridis, bluster, cluster, circlize, speedglm, rmarkdown, gridExtra, BiocStyle, slingshot, gprofiler2, GenomeInfoDb, BiocParallel, BiocGenerics, BiocNeighbors, ComplexHeatmap, Seurat (>= 5.0.0), testthat (>= 3.0.0), SingleCellExperiment, SummarizedExperiment |
| Linking To | Rcpp, RcppEigen |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scLANE_1.0.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | scLANE_1.0.0.tgz |
| macOS Binary (arm64) | scLANE_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scLANE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scLANE |
| Bioc Package Browser | https://code.bioconductor.org/browse/scLANE/ |
| Package Short Url | https://bioconductor.org/packages/scLANE/ |
| Package Downloads Report | Download Stats |