diff --git a/R/core_commons.R b/R/core_commons.R
index fa8937b6538e304712e00c4a62091954768d77bc..0e95ac15ea86a299316245254606f4ff522942db 100644
--- a/R/core_commons.R
+++ b/R/core_commons.R
@@ -20,35 +20,37 @@ require.auto <-  function(x){
     }
 }
 
+#qlibrary <- function(libname) {library(as.character(substitute(libname)), quietly=T, warn.conflicts=F, character.only=T )}
+
+## set a default cran r mirror
+#cat(".Rprofile: Setting Goettingen repository\n")
+r = getOption("repos") # hard code the UK repo for CRAN

+r["CRAN"] = "http://ftp5.gwdg.de/pub/misc/cran/"
+options(repos = r)
+rm(r)
+
+
+## load core packages
 require.auto(plyr)
 require.auto(stringr)
 require.auto(reshape2)
 #require.auto(reshape2, quietly=T, warn.conflicts=F)
-require.auto(scales)
 
+## load on purpose after plyr
 require.auto(dplyr)
 
-
 #require.auto(data.table)
 
+## user browser for help
 options(help_type="html")
+
+## plot more characters per line
 options(width=150)
 
 # for sqldf to avoid the use of tckl
 options(gsubfn.engine = "R")
 
 
-##### set the r mirror
-#cat(".Rprofile: Setting Goettingen repository\n")
-r = getOption("repos") # hard code the UK repo for CRAN

-r["CRAN"] = "http://ftp5.gwdg.de/pub/misc/cran/"
-options(repos = r)
-rm(r)
-
-
-
-
-#qlibrary <- function(libname) {library(as.character(substitute(libname)), quietly=T, warn.conflicts=F, character.only=T )}
 
 
 
@@ -77,6 +79,81 @@ unlen <- function(x) length(unique(x))
 pp <- function(dat) page(dat, method = "print")
 
 
+########################################################################################################################
+#### data.frame manipulation
+
+subsample <- function(df, sampleSize, ...){
+    df[sample(1:nrow(df), min(sampleSize, nrow(df)), ...),]
+}
+
+shuffle <- function(df) df[sample(nrow(df)),]
+
+first <- function(x, n=1) head(x,n)
+
+as.df <- function(dt) as.data.frame(dt)
+
+
+
+rownames2column <- function(df, colname){
+    df <- as.df(df)
+    df$tttt <- rownames(df);
+    rownames(df) <- NULL;
+    rename(df, c(tttt=colname))
+}
+
+
+column2rownames<- function(df, colname){
+#browser()
+    rownames(df) <- ac(df[,colname])
+    df[colname] <- NULL
+    return(df)
+}
+
+## pushing some columns to the right end of a data.frame
+push_right <- function(df, pushColNames){
+    df[,c(setdiff(names(df),pushColNames), pushColNames)]
+}
+
+
+push_left <- function(df, pushColNames){
+    df[,c(pushColNames, setdiff(names(df),pushColNames))]
+}
+
+
+set_names <- function(df, newnames){
+    df<- as.df(df)
+    names(df) <- newnames;
+    return(df)
+}
+
+
+print_head <- function(df, desc=NULL){
+    print(head(df))
+    return(df)
+}
+
+
+fac2char <- function(mydata, convert=names(mydata)[sapply(mydata, is.factor)]){
+    if(length(convert)==0)
+        return(mydata)
+
+    inputColOrder <- names(mydata)
+
+    convertData <- subset(mydata, select= names(mydata)%in%convert)
+    convertData <- as.data.frame(lapply(convertData, as.character), stringsAsFactors = FALSE)
+
+    keepData <-  subset(mydata, select=!(names(mydata)%in%convert))
+    newdata <- cbind(convertData, keepData)
+    newdata <- newdata[,inputColOrder]
+
+    return(newdata)
+}
+
+
+## workaround for biomart
+## Deprecated: load dplyr after biomart to avoid this problem
+#dselect <- function(...) dplyr::select(...)
+
 
 ########################################################################################################################
 #### File System
diff --git a/R/datatable_utils.R b/R/datatable_utils.R
index 3a7733d536a1337671522994c43104ab32e7a901..7b9214d01dbac7c5eb2cf29cbdfbc70e6c1660b9 100644
--- a/R/datatable_utils.R
+++ b/R/datatable_utils.R
@@ -1,4 +1,4 @@
-    require.auto(data.table)
+require.auto(data.table)
 
 
 dt.merge <- function(dfA, dfB, by=intersect(names(dfA), names(dfB)) , ...)  {
diff --git a/R/df_utils.R b/R/df_utils.R
deleted file mode 100644
index 1bf549ac28a400835ca241d49018ff13fffb4c54..0000000000000000000000000000000000000000
--- a/R/df_utils.R
+++ /dev/null
@@ -1,77 +0,0 @@
-
-
-subsample <- function(df, sampleSize, ...){
-    df[sample(1:nrow(df), min(sampleSize, nrow(df)), ...),]
-}
-
-shuffle <- function(df) df[sample(nrow(df)),]
-
-first <- function(x, n=1) head(x,n)
-
-as.df <- function(dt) as.data.frame(dt)
-
-
-## small wrappers
-
-
-
-
-rownames2column <- function(df, colname){
-    df <- as.df(df)
-    df$tttt <- rownames(df);
-    rownames(df) <- NULL;
-    rename(df, c(tttt=colname))
-}
-
-column2rownames<- function(df, colname){
-#browser()
-    rownames(df) <- ac(df[,colname])
-    df[colname] <- NULL
-    return(df)
-}
-
-## pushing some columns to the right end of a data.frame
-push_right <- function(df, pushColNames){
-    df[,c(setdiff(names(df),pushColNames), pushColNames)]
-}
-
-push_left <- function(df, pushColNames){
-    df[,c(pushColNames, setdiff(names(df),pushColNames))]
-}
-
-set_names <- function(df, newnames){
-    df<- as.df(df)
-    names(df) <- newnames;
-    return(df)
-}
-
-
-## dplyr utilities
-
-print_head <- function(df, desc=NULL){
-    print(head(df))
-    return(df)
-}
-
-
-fac2char <- function(mydata, convert=names(mydata)[sapply(mydata, is.factor)]){
-    if(length(convert)==0)
-        return(mydata)
-
-    inputColOrder <- names(mydata)
-
-    convertData <- subset(mydata, select= names(mydata)%in%convert)
-    convertData <- as.data.frame(lapply(convertData, as.character), stringsAsFactors = FALSE)
-
-    keepData <-  subset(mydata, select=!(names(mydata)%in%convert))
-    newdata <- cbind(convertData, keepData)
-    newdata <- newdata[,inputColOrder]
-
-    return(newdata)
-}
-
-
-## workaround for biomart
-dselect <- function(...) dplyr::select(...)
-
-
diff --git a/R/ggplot/ggplot_utils.R b/R/ggplot/ggplot_utils.R
index b77ae14f2cef6dc72b391a093942b33f3dd20eec..e613b2405a99a57470214eb5a13fb75bd80081f2 100644
--- a/R/ggplot/ggplot_utils.R
+++ b/R/ggplot/ggplot_utils.R
@@ -1,5 +1,6 @@
 
 require.auto(ggplot2)
+require.auto(scales)