diff --git a/DESCRIPTION b/DESCRIPTION index a564658..aa49604 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,62 +1,77 @@ Package: scLANE Type: Package -Title: Model gene expression over pseudotime with spline-based NB GLMs, GEEs, & GLMMs -Version: 0.6.2 +Title: Model gene expression dynamics with spline-based NB GLMs, GEEs, & GLMMs +Version: 0.7.0 Authors@R: c(person(given = "Jack", family = "Leary", email = "j.leary@ufl.edu", role = c("aut", "cre")), person(given = "Rhonda", family = "Bacher", email = "rbacher@ufl.edu", role = c("ctb", "fnd"))) -Description: This package uses truncated power basis spline models to build flexible, interpretable models of single cell gene expression over pseudotime / latent time. Currently supports negative binomial GLMs, GEEs, & GLMMs. +Description: This package 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. License: MIT + file LICENSE Encoding: UTF-8 LazyData: true RoxygenNote: 7.2.1 Depends: - magrittr, - glm2 + glm2, + magrittr Imports: - dplyr, - foreach, - doParallel, - parallel, + geeM, MASS, - ggplot2, + dplyr, stats, - gamlss, - scales, - splines, - bigstatsr, - broom, + utils, + withr, purrr, tidyr, - geeM, - glmmTMB, - broom.mixed, - tidyselect, furrr, + gamlss, + scales, future, + ggplot2, + splines, + foreach, + glmmTMB, + parallel, + bigstatsr, RcppEigen, + doParallel, + tidyselect, + broom.mixed, Rcpp (>= 1.0.7) URL: https://github.com/jr-leary7/scLANE BugReports: https://github.com/jr-leary7/scLANE/issues Suggests: - rmarkdown, - knitr, - testthat (>= 3.0.0), covr, + ggh4x, + knitr, + irlba, + rlang, + igraph, + Seurat, bluster, cluster, - clusterProfiler, - igraph, - irlba, - slingshot, msigdbr, + rmarkdown, + slingshot, + BiocGenerics, BiocNeighbors, - rlang, - Seurat, + clusterProfiler, + testthat (>= 3.0.0), SingleCellExperiment, - SummarizedExperiment, - BiocGenerics + SummarizedExperiment VignetteBuilder: knitr Config/testthat/edition: 3 LinkingTo: - RcppEigen, - Rcpp + Rcpp, + RcppEigen +biocViews: + RNASeq, + Software, + TimeCourse, + Sequencing, + Regression, + SingleCell, + Visualization, + GeneExpression, + Transcriptomics, + DifferentialExpression diff --git a/NAMESPACE b/NAMESPACE index e6a60d0..a858874 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,6 +1,7 @@ # Generated by roxygen2: do not edit by hand export(clusterGenes) +export(createCellOffset) export(enrichDynamicGenes) export(extractBreakpoints) export(fitGLMM) @@ -25,7 +26,6 @@ importFrom(MASS,negative.binomial) importFrom(MASS,theta.mm) importFrom(Rcpp,sourceCpp) importFrom(bigstatsr,as_FBM) -importFrom(broom,tidy) importFrom(broom.mixed,tidy) importFrom(doParallel,registerDoParallel) importFrom(dplyr,across) @@ -87,6 +87,8 @@ importFrom(parallel,stopCluster) importFrom(purrr,discard) importFrom(purrr,map) importFrom(purrr,map2) +importFrom(purrr,map_chr) +importFrom(purrr,map_dbl) importFrom(purrr,map_dfr) importFrom(purrr,pmap_dfc) importFrom(purrr,reduce) @@ -104,6 +106,7 @@ importFrom(stats,hclust) importFrom(stats,kmeans) importFrom(stats,lm.fit) importFrom(stats,logLik) +importFrom(stats,offset) importFrom(stats,p.adjust) importFrom(stats,p.adjust.methods) importFrom(stats,pchisq) @@ -113,4 +116,6 @@ importFrom(stats,quantile) importFrom(stats,setNames) importFrom(tidyr,pivot_longer) importFrom(tidyselect,everything) +importFrom(utils,tail) +importFrom(withr,with_output_sink) useDynLib(scLANE, .registration = TRUE)