dagLogo: dagLogo
Version 1.14.0

Visualize significant conserved amino acid sequence pattern in groups based on probability theory.

Browse man pages Browse package API and functions Browse package files

AuthorJianhong Ou, Alexey Stukalov, Niraj Nirala, Usha Acharya, Lihua Julie Zhu
Bioconductor views SequenceMatching Visualization
Date of publicationNone
MaintainerJianhong Ou <jianhong.ou@umassmed.edu>
LicenseGPL (>=2)
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("dagLogo")

Man pages

buildBackgroundModel: build background model
colorsets: retrieve color setting for logo
dagBackground: Class '"dagBackground"'
dagHeatmap: plot heatmap for test results
dagLogo: plot sequence logo for test results
dagLogo-package: Visualize significant conserved amino acid sequence pattern...
dagPeptides: Class '"dagPeptides"'
ecoli.proteome: the subset proteome of Escherichia coli
fetchSequence: fetch sequence by id
formatSequence: prepare an object of dagPeptides from sequences
nameHash: convert group name to a single character
prepareProteome: prepare proteome for background building
Proteome: Class '"Proteome"'
proteome.example: the subset proteome of fruit fly
seq.example: example object of dagPeptides
testDAU: DAU test
testDAUresults: Class '"testDAUresults"'

Functions

Proteome-class Man page
buildBackgroundModel Man page Source code
colorsets Man page Source code
dagBackground-class Man page
dagHeatmap Man page Source code
dagLogo Man page Source code
dagLogo-package Man page
dagPeptides-class Man page
ecoli.proteome Man page
fetchSequence Man page Source code
formatSequence Man page Source code
nameHash Man page Source code
prepareProteome Man page Source code
proteome.example Man page
seq.example Man page
testDAU Man page Source code
testDAUresults-class Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/allclass.R
R/buildBackgroundModel.R
R/dagLogo.R
R/fetchSequence.R
R/formatSequence.R
R/prepareProteome.R
R/testDAU.R
build
build/vignette.rds
data
data/datalist
data/ecoli.proteome.rda
data/proteome.example.rda
data/seq.example.rda
inst
inst/doc
inst/doc/dagLogo.R
inst/doc/dagLogo.Rmd
inst/doc/dagLogo.html
inst/extdata
inst/extdata/HUMAN.fasta
inst/extdata/cap.fasta
inst/extdata/dagLogoTestData.csv
inst/extdata/grB.txt
inst/extdata/peptides4dagLogo.csv
inst/extdata/sample_seq.fasta
inst/extdata/script.txt
inst/extdata/test.data.txt
man
man/Proteome.Rd
man/buildBackgroundModel.Rd
man/colorsets.Rd
man/dagBackground.Rd
man/dagHeatmap.Rd
man/dagLogo-package.Rd
man/dagLogo.Rd
man/dagPeptides.Rd
man/ecoli.proteome.Rd
man/fetchSequence.Rd
man/formatSequence.Rd
man/nameHash.Rd
man/prepareProteome.Rd
man/proteome.example.Rd
man/seq.example.Rd
man/testDAU.Rd
man/testDAUresults.Rd
tests
tests/runTests.R
tests/testthat
tests/testthat/test_DAGtest.R
tests/testthat/test_buildBackgroundModel.R
tests/testthat/test_fetchSequence.R
vignettes
vignettes/bibliography.bib
vignettes/dagLogo.Rmd
dagLogo documentation built on May 20, 2017, 10:59 p.m.