Package Homepage: http://bioconductor.org/packages/devel/bioc/html/customProDB.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=customProDB
CustomProDB enables the easy generation of customized databases from RNA-Seq data for proteomics search. It bridges genomics and proteomics studies and facilitates cross-omics data integration.
Database search is the most widely used approach for peptide and protein identification in mass- spectrometry-based proteomics studies. Sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in the samples and thus improve protein identification. More importantly, single nucleotide variations, short insertion and deletions and novel junctions identified from RNA-Seq data make protein databases more complete and sample-specific.
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("customProDB")Alternatively, you can install the latest version from github using devtools:
# install.packages("devtools")
devtools::install_github("chambm/customProDB")To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("customProDB")