Tools used for analysis and interpretation of foriegn DNA integration elements, such as retroviruses, retroviral-based gene therapy vectors, retrotransposons, or DNA oligos incorporated into a host genome by a Non-Homologous End Joining pathway.
Functions contained in the
gintools package can be separated into different catagories:
Nucleotide sequence processing - managing nucleotide sequence data from machine output, including demultiplexing, trimming, filtering, and consolidating. Alignment can be handled by the user's preferred sequence aligner (BLAT, BWA, ...).
Alignment interpretation - interpret alignment information from PSL or SAM/BAM inputs. Identify important locations, standarize across samples, or resolve edges of observed nucleotide alignments to help reduce noise inherent in the data from PCR amplification and sequencing.
Analytics - functions designed to assist in analysis of processed data. Track observations across specimens, determine abundances of clones, or consolidate data into a summary of observations.
Utilities - functions designed to assist with the other catagories and serve to make seemingly simple operations just that.
gintools, simply run the following command within an R session:
devtools::install_github("https://github.com/cnobles/gintools.git") # Or devtools::install_github("cnobles/gintools")
gintools package depends on
R 3.2 or higher and will
Import the following packages during installation unless they are already present:
The following packages are suggested for increased utility:
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