diff --git a/R/bio/bioinfo_commons.R b/R/bio/bioinfo_commons.R
index 8344df8e84aa8df3b670e911fd46af6d894a815c..d291b567c6b23c9c07f89aa8ed093259a49856cf 100644
--- a/R/bio/bioinfo_commons.R
+++ b/R/bio/bioinfo_commons.R
@@ -5,7 +5,7 @@
 #loadpack(Biostrings)
 
 ## install Biostrings if not yet there
-.inst_pack("Biostrings")
+install_package("Biostrings")
 
 
 read.fasta <- function(fileName){
@@ -40,7 +40,7 @@ write_fasta <- function(seq_names, sequences, file){
 }
 
 
-getSeqLengthFromFasta <- function(fileName){
+get_sequence_lengths <- function(fileName){
     assembly <- mutate(read_fasta(fileName), seq_len=nchar(Sequence))
     assembly$Sequence = NULL
     return(assembly)
@@ -67,10 +67,6 @@ write_bed <- function(bedData, file){
     options(scipen=oldScipen)
 
 }
-write.bed <- function(bedData, file){
-    warning("Deprecated: use write_bed instead!")
-    write_bed(bedData, file)
-}
 
 ## reload to fix rename overloading
 #reload_dplyr()
diff --git a/R/core_commons.R b/R/core_commons.R
index 2e5000b0fda0f722903d58c25d86ccc13c959c39..242f040f41640ed5c29bb967d49184c8140b1fe0 100644
--- a/R/core_commons.R
+++ b/R/core_commons.R
@@ -53,7 +53,7 @@ require_auto <-  function(x){
 }
 
 ## externalized installer to also allow for installation without loading
-.inst_pack <- function(x){
+install_package <- function(x){
     if(!isTRUE(x %in% .packages(all.available=TRUE)) && any(available.packages()[,1]==x)) {
         # update.packages(ask=F) # update dependencies, if any.
         eval(parse(text=paste("install.packages('", x, "')", sep="")))
@@ -73,7 +73,7 @@ require_auto <-  function(x){
 load_pack <-  function(x, warn_conflicts=T){
     x <- as.character(substitute(x));
 
-   .inst_pack(x)
+   install_package(x)
 
     ## load it using a library function so that loadpack errors if package is still not ins
     eval(parse(text=paste("library(", x, ",  quietly=T, warn.conflicts=", warn_conflicts, ")", sep="")))
@@ -84,7 +84,7 @@ loadpack <-  function(x, warn_conflicts=T){
 
     x <- as.character(substitute(x));
 
-   .inst_pack(x)
+   install_package(x)
 
     ## load it using a library function so that loadpack errors if package is still not ins
     eval(parse(text=paste("library(", x, ",  quietly=T, warn.conflicts=", warn_conflicts, ")", sep="")))