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Merge branch 'release/v1.1.2'
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JulieBvs committed Nov 9, 2021
2 parents 80b571d + 970b8f0 commit 98879fa
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8 changes: 4 additions & 4 deletions DESCRIPTION
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Package: scigenex
Type: Package
Title: The scigenex package (Single-Cell Informative GENe Explorer)
Version: 1.0.2
Version: 1.1.2
Date: 2020-07-22
Author: J. Bavais, Aurelie Bergon, Fabrice Lopez, Julien Textoris, Samuel Granjeaud, Lionel Spinelli and Denis Puthier
Maintainer: J. Bavais <[email protected]>
Depends: R (>= 4.0.0), methods, testthat
Imports: reshape2, ggplot2, magrittr, dplyr, igraph, MCL
Collate: dbfmcl_main.R zzz.R
Depends: R (>= 4.0.0), methods, grDevices, stats, utils, dplyr, ggplot2, reshape2, magrittr, testthat, igraph, MCL, iheatmapr
Imports: reshape2, ggplot2, magrittr, dplyr, igraph, gprofiler2, plotly
Collate: dbfmcl_main.R zzz.R import_package.R
Description: The scigenex package (Single-Cell Informative GENe Explorer) proposes a set of functions to extract informative genes from a scRNA-seq experiment, search and store clusters of co-expressed genes. These clusters are annotated and can be mapped onto UMAP or t-SNE diagram to functionally annotate cell populations.
biocViews: Clustering, Classification, Transcriptomics, SingleCell, ReportWriting, GeneRegulation
License: GPL-3
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109 changes: 77 additions & 32 deletions NAMESPACE
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if(.Platform$OS.type == "windows"){
useDynLib("scigenex.dll")
}else{
useDynLib("scigenex")
}

importClassesFrom(methods, character, list, matrix, vector)
importMethodsFrom(methods, show)

importFrom("grDevices", "colorRampPalette")
importFrom("methods", "new", "slot", "slotNames")
importFrom("stats", "sd", dist, hclust, heatmap, median, rnorm)
importFrom("utils", "object.size", "read.table", "write.table", "read.csv")
importFrom(dplyr, summarise, group_by)
importFrom(ggplot2, ggplot, theme_bw,
facet_grid, geom_line, aes,
theme, scale_fill_gradientn, geom_tile,
element_text, element_blank)
importFrom(reshape2, melt)
importFrom(magrittr, '%>%')
importFrom(testthat, expect_equal)
exportClasses("ClusterSet")

export(DBFMCL,
DBF,
mcl_system_cmd,
get_data_4_DBFMCL,
plot_clust,
load_seurat,
write_clust,
VERBOSITY_SCIGENEX)

# Generated by roxygen2: do not edit by hand

export(DBF)
export(DBFMCL)
export(enrich_analysis)
export(enrich_viz)
export(get_data_4_DBFMCL)
export(load_seurat)
export(mcl_system_cmd)
export(plot_clust)
export(plot_dist)
export(plot_heatmap)
export(top_genes)
export(write_clust)
exportClasses(ClusterSet)
exportMethods(dim)
exportMethods(ncol)
exportMethods(nrow)
importFrom(dplyr,distinct)
importFrom(dplyr,group_by)
importFrom(dplyr,summarise)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_linetype_manual)
importFrom(ggplot2,scale_size_manual)
importFrom(ggplot2,stat_density)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(gprofiler2,gost)
importFrom(gprofiler2,gostplot)
importFrom(grDevices,colorRampPalette)
importFrom(igraph,as_adj)
importFrom(igraph,graph_from_data_frame)
importFrom(iheatmapr,add_col_labels)
importFrom(iheatmapr,add_col_title)
importFrom(iheatmapr,add_row_labels)
importFrom(iheatmapr,add_row_title)
importFrom(iheatmapr,main_heatmap)
importFrom(iheatmapr,modify_layout)
importFrom(magrittr,"%>%")
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,signature)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(plotly,layout)
importFrom(reshape2,melt)
importFrom(stats,as.dist)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,heatmap)
importFrom(stats,median)
importFrom(stats,rnorm)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(testthat,expect_equal)
importFrom(utils,object.size)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,write.table)
importMethodsFrom(methods,show)
useDynLib(scigenex)
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