Biological sequence visualization and auxiliary functions in R.
Consists of two main visualization functions: msavisr() and
pdomvisr().
msavisr() takes FASTA-formatted multiple sequence alignments (MSAs)
as inputs and produces visualizations like the example below:
pdomvisr() takes appropriately formatted tabular data and produces
domain structure diagrams like the one below:
cdsearchr() now enables users to submit protein sequence sets to the
NCBI CD-SEARCH server and retrieve annotations as a data.frame
automatically. Example output below:
NEW as of v0.2.7: fastodf() and fasdirdf() are two small utility
functions that can be used to read in one or more FASTA files into R
as a data.frame. fastodf() can be used to read in a single FASTA
file, while fasdirdf() can be used to read in an entire directory’s
worth of FASTA files into a single data.frame. See ?fastodf and
?fasdirdf for examples.
list_files() is a wrapper around base::list.files() that has been
introduced to account for list.files() including directory names by
default when recursive = FALSE. See ?list_files for clarifications.
Ensure that devtools is
installed. Then execute
devtools::install_github("vragh/seqvisr", build_manual = TRUE, build_vignettes = TRUE)
from within R to install the package. If the manual and package
vignette are not necessary,
build_manual = TRUE, build_vignettes = TRUE can be omitted.
See ?seqvisr, ?msavisr, ?pdomvisr, and ?cdsearchr (from within
R) to access documentation and examples for the main functions. Run
browseVignettes("seqvisr") to access the vignette.
Please cite seqvisr using https://zenodo.org/doi/10.5281/zenodo.6583980.
Released under GPL-3. A copy of the license file can be found in the
file LICENSE (LICENCE is just for R purposes).