Finding the DNA and Protein Sequences of Any Genomic or Proteomic Loci

Using the DNA sequence and gene annotation files provided in 'ENSEMBL' < https://www.ensembl.org/index.html>, the functions implemented in the package try to find the DNA sequences and protein sequences of any given genomic loci, and to find the genomic coordinates and protein sequences of any given protein locations, which are the frequent tasks in the analysis of genomic and proteomic data.


News

CHANGES IN VERSION 0.0.3 (24/01/2018)

  1. As the version 0.0.2 did not solve the issue of creating and writting some files in the folders that they should not be created, more modifications were done in this version, namely putting the DNA sequence file uncompressed from the gz file to the temporary folder.

CHANGES IN VERSION 0.0.2 (23/01/2018)

  1. Changed the function names of the two functions: genomicLocToProteinSequence -> genomicLocsToProteinSequence and genomicLocToWholeDNASequence -> genomicLocsToWholeDNASequence, in order to keep them consistent with other function names.
  2. Removed "utils" from the import list in DESCRIPTION file, because it is not used by the package.
  3. Addressed the issue of creating and writting some files in the folders that they should not be created, as raised by the CRAN staff, by using the temporary folder obtained by tempdir().

VERSION 0.0.1

12/12/2017:the package was accepted and published by CRAN repository. September - November 2017: the package was tested and reviewed. January - May 2017: the package was written.

Reference manual

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install.packages("geno2proteo")

0.0.3 by Yaoyong Li, 3 years ago


Browse source code at https://github.com/cran/geno2proteo


Authors: Yaoyong Li


Documentation:   PDF Manual  


Artistic-2.0 license


Imports S4Vectors, BiocGenerics, GenomicRanges, IRanges, R.utils, RUnit

System requirements: Perl (>= 2.0.0)


See at CRAN