release v1.0

.Rbuildignore

@@ -1,3 +1,4 @@
 ^surf\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^README.Rmd

DESCRIPTION

@@ -2,13 +2,18 @@ Package: surf
 Type: Package
 Title: Statistical Utility for RBP (RNA binding protein) Functions
 Version: 0.0.0.9000
-Date: 2019-08-30
+Date: 2020-12-12
 Authors@R: 
     person(given = "Fan",
            family = "Chen",
            role = c("aut", "cre"),
            email = "[email protected]",
            comment = c(ORCID = "0000-0003-4508-6023"))
+    person(given = "Sunduz",
+           family = "Keles",
+           role = c("aut", "cre"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0001-9048-0922"))
 Description: 
     The marriage of RNA-seq and CLIP-seq for data-supported hypothesis for RBP functions.
 URL: https:github.com/fchen365/surf
@@ -23,6 +28,7 @@ Imports:
     arm,
     doMC,
     MASS,
+    withr,
     rlang,
     dplyr,
     tidyr,
@@ -34,17 +40,24 @@ Imports:
     ggpubr,
     Matrix,
     AUCell,
+    IRanges,
     methods,
     stringr,
     forcats,
     ggplot2,
+    foreach,
+    parallel,
     reshape2,
     magrittr,
     Rsubread,
+    S4Vectors,
     ensembldb,
     tidyverse,
     data.table,
     rtracklayer,
+    BiocGenerics,
+    BiocParallel,
+    GenomicRanges,
     SummarizedExperiment,
 Suggests:
     knitr,

NAMESPACE

@@ -25,13 +25,44 @@ exportMethods(heatmapAUC)
 exportMethods(plotDispFunc)
 exportMethods(sampleData)
 exportMethods(volcano.plot)
-importClassesFrom(SummarizedExperiment,SummarizedExperiment)
+import(BiocGenerics)
+import(DEXSeq)
+import(GenomicRanges)
+import(SummarizedExperiment)
+import(foreach)
+importFrom(BiocParallel,MulticoreParam)
+importFrom(BiocParallel,bplapply)
+importFrom(BiocParallel,bpparam)
+importFrom(BiocParallel,multicoreWorkers)
+importFrom(IRanges,DataFrameList)
+importFrom(IRanges,FactorList)
+importFrom(IRanges,IRanges)
+importFrom(S4Vectors,"mcols<-")
+importFrom(S4Vectors,"metadata<-")
+importFrom(S4Vectors,DataFrame)
+importFrom(S4Vectors,Hits)
+importFrom(S4Vectors,List)
+importFrom(S4Vectors,cbind)
+importFrom(S4Vectors,elementNROWS)
+importFrom(S4Vectors,from)
+importFrom(S4Vectors,head)
+importFrom(S4Vectors,mcols)
+importFrom(S4Vectors,metadata)
+importFrom(S4Vectors,queryHits)
+importFrom(S4Vectors,rbind)
+importFrom(S4Vectors,to)
+importFrom(doParallel,registerDoParallel)
+importFrom(doParallel,stopImplicitCluster)
 importFrom(dplyr,arrange)
+importFrom(dplyr,bind_rows)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,n)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
+importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,element_blank)
@@ -58,13 +89,25 @@ importFrom(ggplot2,stat_function)
 importFrom(ggplot2,stat_summary)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
+importFrom(ggplot2,unit)
 importFrom(ggplot2,vars)
 importFrom(magrittr,"%>%")
 importFrom(methods,as)
 importFrom(methods,is)
 importFrom(methods,new)
+importFrom(methods,selectMethod)
+importFrom(methods,slot)
+importFrom(parallel,detectCores)
 importFrom(rlang,.data)
+importFrom(stats,aggregate)
+importFrom(stats,binomial)
+importFrom(stats,dist)
+importFrom(stats,hclust)
+importFrom(stats,na.omit)
+importFrom(stats,p.adjust)
+importFrom(stats,pnorm)
+importFrom(stats,quantile)
 importFrom(stats,setNames)
-importMethodsFrom(SummarizedExperiment,assay)
-importMethodsFrom(SummarizedExperiment,assayNames)
-importMethodsFrom(SummarizedExperiment,assays)
+importFrom(stats,weighted.mean)
+importFrom(tidyr,pivot_longer)
+importFrom(tidyr,pivot_wider)