Merge pull request #66 from seoanezonjic/revert-65-aberrant_expression

Revert "Aberrant expression"

DESCRIPTION

@@ -65,62 +65,54 @@ Suggests:
     testthat (>= 3.0.0)
 VignetteBuilder: knitr
 Imports: 
-    ReactomePA (>= 1.46.0),
-    limma (>= 3.58.0),
-    edgeR (>= 4.0.15),
-    NOISeq (>= 2.46.0),
-    biomaRt (>= 2.58.0),
-    topGO (>= 2.54.0),
-    diffcoexp (>= 1.22.0),
-    DT (>= 0.30),
-    ggplot2 (>= 3.4.4),
-    stringr (>= 1.5.0),
-    WGCNA (>= 1.72.1),
-    dplyr (>= 1.1.3),
-    BiocGenerics (>= 0.48.0),
-    enrichplot (>= 1.22.0),
-    rmarkdown (>= 2.25),
-    stats (>= 4.3.1),
-    Biobase (>= 2.62.0),
-    DESeq2 (>= 1.42.0),
-    ROCR (>= 1.0.11),
-    data.table (>= 1.14.8),
-    knitr (>= 1.44),
-    magrittr (>= 2.0.3),
-    SummarizedExperiment (>= 1.32.0),
-    miRBaseVersions.db (>= 1.1.0),
-    grDevices (>= 4.3.1),
-    graphics (>= 4.3.1),
-    utils (>= 4.3.1),
-    BiocParallel (>= 1.36.0),
-    MKinfer (>= 1.1),
-    matrixStats (>= 1.0.0),
-    ggupset (>= 0.3.0),
-    rlang (>= 1.1.1),
-    plyr (>= 1.8.9),
-    tidyr (>= 1.3.0),
-    GO.db (>= 3.18.0),
-    Matrix (>= 1.6.1.1),
-    fastcluster (>= 1.2.3),
-    DOSE (>= 3.28.0),
-    heatmaply (>= 1.5.0),
-    EnhancedVolcano (>= 1.20.0),
-    ggrepel (>= 0.9.4),
-    clusterProfiler (>= 4.11.0),
-    GenomicRanges (>= 1.54.0),
-    GenomicFeatures (>= 1.54.0),
-    tximport (>= 1.30.0),
-    annotatr (>= 1.28.0),
-    ggridges (>= 0.5.4),
-    FactoInvestigate (>= 1.8),
-    FactoMineR (>= 2.9),
-    cowplot (>= 1.1.1),
-    S4Vectors (>= 0.40.0),
-    OUTRIDER (>= 1.20.0),
-    MatrixGenerics (>= 1.14.0),
-    GenomeInfoDb (>= 1.38.0),
-    yaml (>= 2.3.7),
-    rtracklayer (>= 1.62.0),
-    AnnotationDbi (>= 1.64.0),
-    htmlreportR (>= 1.0.0)
+    ReactomePA,
+    limma,
+    edgeR,
+    NOISeq,
+    biomaRt,
+    topGO,
+    diffcoexp,
+    DT,
+    ggplot2,
+    stringr,
+    WGCNA,
+    dplyr,
+    AnnotationDbi,
+    BiocGenerics,
+    enrichplot,
+    rmarkdown,
+    stats,
+    Biobase,
+    DESeq2,
+    ROCR,
+    data.table,
+    knitr,
+    magrittr,
+    SummarizedExperiment,
+    miRBaseVersions.db,
+    grDevices,
+    graphics,
+    utils,
+    BiocParallel,
+    MKinfer,
+    matrixStats,
+    ggupset,
+    rlang,
+    plyr,
+    tidyr,
+    GO.db,
+    Matrix,
+    fastcluster,
+    DOSE,
+    heatmaply,
+    EnhancedVolcano, 
+    ggrepel,
+    clusterProfiler,
+    GenomicRanges,
+    GenomicFeatures,
+    tximport,
+    annotatr,
+    ggridges,
+    FactoInvestigate,
+    FactoMineR
 Config/testthat/edition: 3

NAMESPACE

@@ -2,49 +2,33 @@
 
 export(acc)
 export(degsynth)
-export(filter_counts)
 export(fmeasure)
-export(format_aberrants)
-export(format_for_report)
-export(get_aberrants)
-export(get_bcv)
-export(get_counts_correlation)
-export(get_gene_sample_correlations)
-export(get_ods_results)
 export(get_org_db)
 export(get_organism_table)
 export(get_stats)
 export(get_stats_from_cm)
 export(install_DEgenes_hunter)
 export(load_and_parse_gmt)
 export(load_synth_dataset)
-export(main_abgenes_Hunter)
 export(main_clusters_to_enrichment)
 export(main_degenes_Hunter)
 export(main_functional_hunter)
-export(merge_bam_stats)
-export(merge_counts)
 export(multienricher_gsea)
 export(multienricher_ora)
 export(multienricher_topGO)
 export(parse_pseudocounts)
 export(ppv)
-export(preprocess_gtf)
 export(recall)
 export(rtable2measures)
-export(run_outrider)
 export(spc)
 export(target_generation)
 export(write_clusters_to_enrichment)
 export(write_df_list_as_tables)
 export(write_enrich_files)
 export(write_expression_report)
 export(write_functional_report)
-import(data.table)
 importClassesFrom(topGO,topGOdata)
 importFrom(AnnotationDbi,keys)
-importFrom(AnnotationDbi,loadDb)
-importFrom(AnnotationDbi,saveDb)
 importFrom(AnnotationDbi,select)
 importFrom(Biobase,assayData)
 importFrom(BiocParallel,MulticoreParam)
@@ -71,41 +55,18 @@ importFrom(GO.db,GOMFANCESTOR)
 importFrom(GO.db,GOMFPARENTS)
 importFrom(GO.db,GOOBSOLETE)
 importFrom(GO.db,GOTERM)
-importFrom(GenomeInfoDb,keepStandardChromosomes)
-importFrom(GenomicFeatures,exonsBy)
 importFrom(GenomicFeatures,makeTxDbFromGFF)
 importFrom(GenomicRanges,makeGRangesFromDataFrame)
 importFrom(MKinfer,boot.t.test)
 importFrom(Matrix,forceSymmetric)
-importFrom(MatrixGenerics,rowQuantiles)
 importFrom(NOISeq,noiseqbio)
 importFrom(NOISeq,readData)
 importFrom(NOISeq,tmm)
-importFrom(OUTRIDER,OUTRIDER)
-importFrom(OUTRIDER,OutriderDataSet)
-importFrom(OUTRIDER,counts)
-importFrom(OUTRIDER,estimateSizeFactors)
-importFrom(OUTRIDER,filterExpression)
-importFrom(OUTRIDER,findEncodingDim)
-importFrom(OUTRIDER,fit)
-importFrom(OUTRIDER,normalizationFactors)
-importFrom(OUTRIDER,plotAberrantPerSample)
-importFrom(OUTRIDER,plotCountCorHeatmap)
-importFrom(OUTRIDER,plotCountGeneSampleHeatmap)
-importFrom(OUTRIDER,plotEncDimSearch)
-importFrom(OUTRIDER,results)
-importFrom(OUTRIDER,theta)
 importFrom(ROCR,performance)
 importFrom(ROCR,prediction)
 importFrom(ReactomePA,enrichPathway)
 importFrom(ReactomePA,gsePathway)
-importFrom(S4Vectors,endoapply)
-importFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(SummarizedExperiment,assay)
-importFrom(SummarizedExperiment,colData)
-importFrom(SummarizedExperiment,mcols)
-importFrom(SummarizedExperiment,rowData)
-importFrom(SummarizedExperiment,rowRanges)
 importFrom(WGCNA,allowWGCNAThreads)
 importFrom(WGCNA,binarizeCategoricalVariable)
 importFrom(WGCNA,blockwiseModules)
@@ -123,11 +84,7 @@ importFrom(clusterProfiler,gseGO)
 importFrom(clusterProfiler,gseKEGG)
 importFrom(clusterProfiler,merge_result)
 importFrom(clusterProfiler,simplify)
-importFrom(cowplot,background_grid)
-importFrom(cowplot,plot_grid)
-importFrom(cowplot,theme_cowplot)
 importFrom(data.table,as.data.table)
-importFrom(data.table,fread)
 importFrom(data.table,merge.data.table)
 importFrom(data.table,rbindlist)
 importFrom(data.table,setnames)
@@ -137,7 +94,6 @@ importFrom(dplyr,between)
 importFrom(dplyr,desc)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
-importFrom(dplyr,left_join)
 importFrom(dplyr,row_number)
 importFrom(edgeR,DGEList)
 importFrom(edgeR,calcNormFactors)
@@ -155,14 +111,10 @@ importFrom(fastcluster,hclust)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_string)
 importFrom(ggplot2,element_blank)
-importFrom(ggplot2,element_rect)
 importFrom(ggplot2,element_text)
-importFrom(ggplot2,facet_wrap)
 importFrom(ggplot2,fortify)
 importFrom(ggplot2,geom_bar)
-importFrom(ggplot2,geom_boxplot)
 importFrom(ggplot2,geom_count)
-importFrom(ggplot2,geom_histogram)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_text)
 importFrom(ggplot2,geom_tile)
@@ -172,18 +124,13 @@ importFrom(ggplot2,ggplot_gtable)
 importFrom(ggplot2,ggsave)
 importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,guide_colorbar)
-importFrom(ggplot2,guide_legend)
 importFrom(ggplot2,guides)
-importFrom(ggplot2,labs)
-importFrom(ggplot2,scale_color_brewer)
 importFrom(ggplot2,scale_colour_gradientn)
 importFrom(ggplot2,scale_fill_gradient2)
 importFrom(ggplot2,scale_shape_manual)
 importFrom(ggplot2,scale_x_continuous)
-importFrom(ggplot2,scale_x_log10)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,theme)
-importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,theme_classic)
 importFrom(ggplot2,theme_light)
 importFrom(ggplot2,theme_minimal)
@@ -213,7 +160,6 @@ importFrom(miRBaseVersions.db,miRBaseVersions.db)
 importFrom(plyr,rbind.fill)
 importFrom(rlang,.data)
 importFrom(rmarkdown,render)
-importFrom(rtracklayer,import)
 importFrom(stats,as.dist)
 importFrom(stats,complete.cases)
 importFrom(stats,cor)
@@ -234,7 +180,6 @@ importFrom(stats,setNames)
 importFrom(stats,var)
 importFrom(stringr,str_remove)
 importFrom(tidyr,unite)
-importFrom(tools,file_path_sans_ext)
 importFrom(topGO,annFUN)
 importFrom(tximport,tximport)
 importFrom(utils,assignInNamespace)