resovle line char notes and some warnings

.gitignore

@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

NAMESPACE

@@ -62,35 +62,17 @@ exportMethods(scale_abundance)
 exportMethods(tidybulk)
 exportMethods(tidybulk_SAM_BAM)
 import(SummarizedExperiment)
-import(broom)
-import(class)
 import(e1071)
-import(edgeR)
 import(lifecycle)
-import(limma)
 import(lme4)
 import(methods)
 import(parallel)
 import(preprocessCore)
 import(readr)
-import(sva)
 import(tibble)
-importFrom(AnnotationDbi,mapIds)
-importFrom(DESeq2,DESeq)
-importFrom(DESeq2,DESeqDataSet)
-importFrom(DESeq2,DESeqDataSetFromMatrix)
-importFrom(DESeq2,results)
 importFrom(GenomicRanges,makeGRangesListFromDataFrame)
 importFrom(Matrix,colSums)
-importFrom(Rtsne,Rtsne)
-importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,metadata)
-importFrom(Seurat,CreateSeuratObject)
-importFrom(Seurat,FindClusters)
-importFrom(Seurat,FindNeighbors)
-importFrom(Seurat,FindVariableFeatures)
-importFrom(Seurat,RunPCA)
-importFrom(Seurat,ScaleData)
 importFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
@@ -99,8 +81,6 @@ importFrom(SummarizedExperiment,rowRanges)
 importFrom(betareg,betareg)
 importFrom(boot,logit)
 importFrom(broom,tidy)
-importFrom(clusterProfiler,GSEA)
-importFrom(clusterProfiler,enricher)
 importFrom(dplyr,across)
 importFrom(dplyr,anti_join)
 importFrom(dplyr,arrange)
@@ -135,17 +115,10 @@ importFrom(dplyr,summarise)
 importFrom(dplyr,summarise_all)
 importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
-importFrom(edgeR,DGEList)
-importFrom(edgeR,calcNormFactors)
-importFrom(edgeR,estimateDisp)
-importFrom(edgeR,filterByExpr)
 importFrom(functional,Compose)
-importFrom(glmmSeq,glmmSeq)
 importFrom(glmmTMB,glmmTMBControl)
 importFrom(lifecycle,deprecate_soft)
 importFrom(lifecycle,deprecate_warn)
-importFrom(limma,makeContrasts)
-importFrom(limma,normalizeQuantiles)
 importFrom(magrittr,"%$%")
 importFrom(magrittr,"%>%")
 importFrom(magrittr,divide_by)
@@ -155,17 +128,11 @@ importFrom(magrittr,multiply_by)
 importFrom(magrittr,set_colnames)
 importFrom(magrittr,set_rownames)
 importFrom(matrixStats,colSds)
-importFrom(msigdbr,msigdbr)
-importFrom(msigdbr,msigdbr_species)
-importFrom(org.Hs.eg.db,org.Hs.eg.db)
-importFrom(org.Mm.eg.db,org.Mm.eg.db)
 importFrom(parallel,clusterExport)
 importFrom(parallel,makeCluster)
 importFrom(parallel,mclapply)
 importFrom(pbapply,pblapply)
 importFrom(pbmcapply,pbmclapply)
-importFrom(preprocessCore,normalize.quantiles.determine.target)
-importFrom(preprocessCore,normalize.quantiles.use.target)
 importFrom(purrr,as_mapper)
 importFrom(purrr,map)
 importFrom(purrr,map2)
@@ -221,8 +188,6 @@ importFrom(survival,coxph)
 importFrom(survival,survdiff)
 importFrom(survminer,ggsurvplot)
 importFrom(survminer,surv_fit)
-importFrom(sva,ComBat)
-importFrom(sva,ComBat_seq)
 importFrom(tibble,as_tibble)
 importFrom(tibble,enframe)
 importFrom(tibble,rowid_to_column)
@@ -243,7 +208,6 @@ importFrom(ttservice,bind_rows)
 importFrom(utils,capture.output)
 importFrom(utils,data)
 importFrom(utils,head)
+importFrom(utils,install.packages)
 importFrom(utils,packageDescription)
 importFrom(utils,tail)
-importFrom(uwot,tumap)
-importFrom(widyr,pairwise_cor)