RWebLogo: plotting custom sequence logos
Version 1.0.3

RWebLogo is a wrapper for the WebLogo python package that allows generating of customised sequence logos. Sequence logos are graphical representations of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences). Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.

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AuthorOmar Wagih
Date of publication2014-08-10 23:50:59
MaintainerOmar Wagih <wagih@ebi.ac.uk>
LicenseBSD_3_clause + file LICENSE
Version1.0.3
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RWebLogo")

Getting started

README.md

Popular man pages

weblogo: Plot a sequence logo

Man pages

weblogo: Plot a sequence logo

Functions

check Source code
check.class Source code
cmd.add Source code
python.valid Source code
weblogo Man page Source code
writeLines Source code

Files

inst
inst/extdata
inst/extdata/weblogo-3.3
inst/extdata/weblogo-3.3/build_test.sh
inst/extdata/weblogo-3.3/cap.fa
inst/extdata/weblogo-3.3/corebio
inst/extdata/weblogo-3.3/corebio/moremath.py
inst/extdata/weblogo-3.3/corebio/__init__.pyc
inst/extdata/weblogo-3.3/corebio/seq_io
inst/extdata/weblogo-3.3/corebio/seq_io/__init__.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/msf_io.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/__init__.py
inst/extdata/weblogo-3.3/corebio/seq_io/nexus_io.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/clustal_io.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/nbrf_io.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/table_io.py
inst/extdata/weblogo-3.3/corebio/seq_io/plain_io.py
inst/extdata/weblogo-3.3/corebio/seq_io/intelligenetics_io.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/fasta_io.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/array_io.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/plain_io.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/table_io.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/intelligenetics_io.py
inst/extdata/weblogo-3.3/corebio/seq_io/stockholm_io.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/null_io.py
inst/extdata/weblogo-3.3/corebio/seq_io/phylip_io.py
inst/extdata/weblogo-3.3/corebio/seq_io/array_io.py
inst/extdata/weblogo-3.3/corebio/seq_io/fasta_io.py
inst/extdata/weblogo-3.3/corebio/seq_io/stockholm_io.py
inst/extdata/weblogo-3.3/corebio/seq_io/nexus_io.py
inst/extdata/weblogo-3.3/corebio/seq_io/genbank_io.py
inst/extdata/weblogo-3.3/corebio/seq_io/nbrf_io.py
inst/extdata/weblogo-3.3/corebio/seq_io/msf_io.py
inst/extdata/weblogo-3.3/corebio/seq_io/clustal_io.py
inst/extdata/weblogo-3.3/corebio/seq_io/phylip_io.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/genbank_io.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/_nexus
inst/extdata/weblogo-3.3/corebio/seq_io/_nexus/Trees.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/_nexus/__init__.pyc
inst/extdata/weblogo-3.3/corebio/seq_io/_nexus/__init__.py
inst/extdata/weblogo-3.3/corebio/seq_io/_nexus/Trees.py
inst/extdata/weblogo-3.3/corebio/seq_io/_nexus/Nodes.py
inst/extdata/weblogo-3.3/corebio/seq_io/_nexus/Nodes.pyc
inst/extdata/weblogo-3.3/corebio/secstruc
inst/extdata/weblogo-3.3/corebio/secstruc/dssp.py
inst/extdata/weblogo-3.3/corebio/secstruc/__init__.py
inst/extdata/weblogo-3.3/corebio/secstruc/stride.py
inst/extdata/weblogo-3.3/corebio/_version.py
inst/extdata/weblogo-3.3/corebio/moremath.pyc
inst/extdata/weblogo-3.3/corebio/__init__.py
inst/extdata/weblogo-3.3/corebio/data.pyc
inst/extdata/weblogo-3.3/corebio/data.py
inst/extdata/weblogo-3.3/corebio/_version.pyc
inst/extdata/weblogo-3.3/corebio/data
inst/extdata/weblogo-3.3/corebio/data/vtml160
inst/extdata/weblogo-3.3/corebio/data/pam120.mat
inst/extdata/weblogo-3.3/corebio/data/blosum45.mat
inst/extdata/weblogo-3.3/corebio/data/blosum80.mat
inst/extdata/weblogo-3.3/corebio/data/dbxref.txt
inst/extdata/weblogo-3.3/corebio/data/blosum100.mat
inst/extdata/weblogo-3.3/corebio/data/blosum50.mat
inst/extdata/weblogo-3.3/corebio/data/blosum62.mat
inst/extdata/weblogo-3.3/corebio/data/blosum40.mat
inst/extdata/weblogo-3.3/corebio/data/blosum35.mat
inst/extdata/weblogo-3.3/corebio/data/pam250.mat
inst/extdata/weblogo-3.3/corebio/data/dist20_comp.mat
inst/extdata/weblogo-3.3/corebio/db
inst/extdata/weblogo-3.3/corebio/db/__init__.py
inst/extdata/weblogo-3.3/corebio/db/scop.py
inst/extdata/weblogo-3.3/corebio/db/astral.py
inst/extdata/weblogo-3.3/corebio/seq.pyc
inst/extdata/weblogo-3.3/corebio/transform.py
inst/extdata/weblogo-3.3/corebio/ssearch_io
inst/extdata/weblogo-3.3/corebio/ssearch_io/blastxml.py
inst/extdata/weblogo-3.3/corebio/ssearch_io/__init__.py
inst/extdata/weblogo-3.3/corebio/ssearch_io/fasta.py
inst/extdata/weblogo-3.3/corebio/matrix.py
inst/extdata/weblogo-3.3/corebio/seq.py
inst/extdata/weblogo-3.3/corebio/utils
inst/extdata/weblogo-3.3/corebio/utils/__init__.pyc
inst/extdata/weblogo-3.3/corebio/utils/__init__.py
inst/extdata/weblogo-3.3/corebio/utils/_which.py
inst/extdata/weblogo-3.3/corebio/utils/deoptparse.py
inst/extdata/weblogo-3.3/corebio/utils/deoptparse.pyc
inst/extdata/weblogo-3.3/corebio/utils/_which.pyc
inst/extdata/weblogo-3.3/corebio/matrix.pyc
inst/extdata/weblogo-3.3/test_weblogo
inst/extdata/weblogo-3.3/test_weblogo/data
inst/extdata/weblogo-3.3/test_weblogo/data/cap.fa
inst/extdata/weblogo-3.3/test_weblogo/data/Rv3829c.fasta
inst/extdata/weblogo-3.3/test_weblogo/data/cox2.msf
inst/extdata/weblogo-3.3/transformseq
inst/extdata/weblogo-3.3/apidocs
inst/extdata/weblogo-3.3/apidocs/index.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.logomath-pysrc.html
inst/extdata/weblogo-3.3/apidocs/weblogolib-module.html
inst/extdata/weblogo-3.3/apidocs/redirect.html
inst/extdata/weblogo-3.3/apidocs/weblogolib._cgi-pysrc.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.logomath.Gamma-class.html
inst/extdata/weblogo-3.3/apidocs/identifier-index.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.color.Color-class.html
inst/extdata/weblogo-3.3/apidocs/module-tree.html
inst/extdata/weblogo-3.3/apidocs/weblogolib._cgi-module.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.colorscheme-pysrc.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.colorscheme.ColorGroup-class.html
inst/extdata/weblogo-3.3/apidocs/weblogolib-pysrc.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.color-module.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.logomath-module.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.GhostscriptAPI-class.html
inst/extdata/weblogo-3.3/apidocs/weblogolib._cgi.Field-class.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.colorscheme-module.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.LogoFormat-class.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.color-pysrc.html
inst/extdata/weblogo-3.3/apidocs/weblogolib._cli-module.html
inst/extdata/weblogo-3.3/apidocs/help.html
inst/extdata/weblogo-3.3/apidocs/weblogolib._cli-pysrc.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.logomath.Dirichlet-class.html
inst/extdata/weblogo-3.3/apidocs/class-tree.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.LogoData-class.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.colorscheme.ColorScheme-class.html
inst/extdata/weblogo-3.3/apidocs/weblogolib.LogoOptions-class.html
inst/extdata/weblogo-3.3/LICENSE.txt
inst/extdata/weblogo-3.3/test_corebio.py
inst/extdata/weblogo-3.3/setup.py
inst/extdata/weblogo-3.3/weblogolib
inst/extdata/weblogo-3.3/weblogolib/htdocs
inst/extdata/weblogo-3.3/weblogolib/htdocs/index.html
inst/extdata/weblogo-3.3/weblogolib/htdocs/examples
inst/extdata/weblogo-3.3/weblogolib/htdocs/examples/lexA.fa
inst/extdata/weblogo-3.3/weblogolib/htdocs/examples/lexA.png
inst/extdata/weblogo-3.3/weblogolib/htdocs/examples/cap_dna.fa
inst/extdata/weblogo-3.3/weblogolib/htdocs/examples/globins.png
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inst/extdata/weblogo-3.3/weblogolib/htdocs/examples/build_examples.sh
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inst/extdata/weblogo-3.3/weblogolib/htdocs/logo.css
inst/extdata/weblogo-3.3/weblogolib/color.py
inst/extdata/weblogo-3.3/weblogolib/logomath.pyc
inst/extdata/weblogo-3.3/weblogolib/logomath.py
inst/extdata/weblogo-3.3/weblogolib/__init__.pyc
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inst/extdata/weblogo-3.3/weblogolib/colorscheme.py
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inst/extdata/weblogo-3.3/weblogolib/_cli.py
inst/extdata/weblogo-3.3/weblogolib/custom_template.eps
inst/extdata/weblogo-3.3/weblogolib/_cli.pyc
inst/extdata/weblogo-3.3/weblogolib/color.pyc
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inst/extdata/weblogo-3.3/weblogolib/colorscheme.pyc
inst/extdata/weblogo-3.3/weblogolib/_cgi.py
inst/extdata/weblogo-3.3/test_weblogo.py
inst/extdata/weblogo-3.3/weblogo
inst/extdata/weblogo-3.3/MANIFEST.in
inst/extdata/weblogo-3.3/README.txt
inst/extdata/weblogo-3.3/PKG-INFO
inst/extdata/example_logo.eps
inst/extdata/example_logo.jpeg
inst/extdata/weblogo-3.3_bkp.zip
inst/extdata/example_data.msf
NAMESPACE
R
R/plotlogo.R
R/RWebLogo.R
README.md
MD5
build
build/logo.png
build/logo.pdf
build/BUILD.R
DESCRIPTION
man
man/weblogo.Rd
LICENSE
CHANGES
RWebLogo documentation built on May 19, 2017, 1:29 p.m.