dagLogo: dagLogo

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

Author
Jianhong Ou, Alexey Stukalov, Niraj Nirala, Usha Acharya, Lihua Julie Zhu
Date of publication
None
Maintainer
Jianhong Ou <jianhong.ou@umassmed.edu>
License
GPL (>=2)
Version
1.12.0

View on Bioconductor

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"'

Files in this package

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