DESCRIPTION

Package: scigenex
Type: Package
Title: The scigenex package (Single-Cell Informative GENe Explorer)
Version: 1.4.11
Date: 2020-07-22
Author: J. Bavais, Sebastien Nin, Lionel Spinelli and Denis Puthier
Maintainer: J. Bavais <julie.bavais@yahoo.fr>
Depends: R (>= 4.0.0), methods
Imports: scales, reshape2, ggplot2, dplyr, igraph, plotly, qlcMatrix, clusterProfiler, org.Hs.eg.db, org.Mm.eg.db, amap, grDevices, stats, utils, magrittr, testthat, iheatmapr, AnnotationDbi, data.table, enrichplot, SeuratObject, pheatmap, Seurat, Matrix, SparseM, ggforce, ggstar, patchwork, biomaRt, ggh4x, WriteXLS, pracma, jinjar, cluster, clValid, DT
Collate: ClusterSet_class.R import_package.R enrichment_analysis.R top_genes.R visualization.R get_data_for_scigenex.R get_genes.R reorder_genes.R utils.R dataset_doc.R plot_profiles.R filter_gene_clusters.R gene_clustering.R select_genes.R Visium_hull.R compare_gene_sets.R cluster_stats.R convert.R plot_spatial.R top_by_go.R dist2border.R clusterset_report.R module_quality_scores.R zzz.R
Description: The scigenex package (Single-Cell Informative GENe Explorer) proposes a set of functions to (i) extract informative genes from a scRNA-seq and Visium experiment, (ii) search clusters of co-expressed genes, (iii) store/manipulate these clusters, (v) and anotate these clusters. These clusters can be mapped onto UMAP or t-SNE diagrams to functionally annotate cell populations.
biocViews: Clustering, Classification, Transcriptomics, SingleCell, ReportWriting, GeneRegulation
License: GPL (>= 3)
VignetteBuilder: knitr
Suggests: covr, RColorBrewer, png, RCurl, clustermole, knitr, rmarkdown, SeuratData, tidyr
LazyLoad: yes
LazyDataCompression: xz
URL: https://github.com/dputhier/scigenex
Packaged: 
RoxygenNote: 7.3.2
Encoding: UTF-8
LazyData: true
Config/testthat/edition: 3