DiffLogo: DiffLogo: A comparative visualisation of sequence motifs
Version 1.6.0

DiffLogo is an easy-to-use tool to visualize motif differences.

AuthorMartin Nettling [aut], Hendrik Treutler [aut, cre], Jan Grau [aut, ctb], Jens Keilwagen [aut, ctb], Stefan Posch [aut], Ivo Grosse [aut]
Bioconductor views MotifAnnotation MultipleComparison SequenceMatching Software Visualization
Date of publicationNone
MaintainerHendrik Treutler <htreutle@ipb-halle.de>
LicenseGPL (>= 2)
Version1.6.0
URL https://github.com/mgledi/DiffLogo/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DiffLogo")

Getting started

README.md

Popular man pages

ASN: ASN alphabet
diffLogo: Draw DiffLogo
diffLogoTable: Draw DiffLogo-table
getPwmFromAlignment: Create PWM from alignment
RNA: RNA alphabet
seqLogo: Draw sequence logo
sumOfAbsICDifferences: sum of absolute information content differences
See all...

All man pages Function index File listing

Man pages

Alphabet: built alphabet
ASN: ASN alphabet
createDiffLogoObject: DiffLogo object
differenceOfICs: normalized information content differences
diffLogo: Draw DiffLogo
diffLogoFromPwm: Draw DiffLogo from PWM
diffLogoTable: Draw DiffLogo-table
DNA: DNA alphabet
getPwmFromAlignment: Create PWM from alignment
informationContent: information content
lossOfAbsICDifferences: the change of information content
normalizedDifferenceOfProbabilities: normalized probability differences
probabilities: probabilities
RNA: RNA alphabet
seqLogo: Draw sequence logo
shannonDivergence: shannon divergence
sumOfAbsICDifferences: sum of absolute information content differences
sumOfAbsProbabilityDifferences: sum of absolute probability differences
sumProbabilities: sum of probabilities, i.e. 1.0

Functions

ASN Man page
Alphabet Man page Source code
DNA Man page
Letter Source code
RNA Man page
addLetter Source code
createDiffLogoObject Man page Source code
diffLogo Man page Source code
diffLogoFromPwm Man page Source code
diffLogoTable Man page Source code
differenceOfICs Man page Source code
getPwmFromAlignment Man page Source code
informationContent Man page Source code
lossOfAbsICDifferences Man page Source code
normalizedDifferenceOfProbabilities Man page Source code
preconditionBaseDistribution Source code
preconditionPWM Source code
preconditionPWMSameSize Source code
preconditionStackHeight Source code
preconditionTransformPWM Source code
probabilities Man page Source code
seqLogo Man page Source code
shannonDivergence Man page Source code
sumOfAbsICDifferences Man page Source code
sumOfAbsProbabilityDifferences Man page Source code
sumProbabilities Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/alphabet.R
R/baseDistrs.R
R/diffSeqLogo.R
R/preconditions.R
R/seqLogo.R
R/stackHeights.R
R/utilities.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/DiffLogoBasics.R
inst/doc/DiffLogoBasics.Rnw
inst/doc/DiffLogoBasics.pdf
inst/extdata
inst/extdata/alignments
inst/extdata/alignments/F-box_bacteria.seq.fa
inst/extdata/alignments/F-box_fungi.seq.fa
inst/extdata/alignments/F-box_metazoa.seq.fa
inst/extdata/alignments/F-box_viridiplantae.seq.fa
inst/extdata/alignments/Mad.txt
inst/extdata/alignments/Max.txt
inst/extdata/alignments/Myc.txt
inst/extdata/alignments/calamodulin_1.txt
inst/extdata/alignments/calamodulin_2.txt
inst/extdata/alignments/phosphorylation_1.txt
inst/extdata/alignments/phosphorylation_2.txt
inst/extdata/alignments/ubiquitination_1.txt
inst/extdata/alignments/ubiquitination_2.txt
inst/extdata/pwm
inst/extdata/pwm/GM12878.txt
inst/extdata/pwm/H1-hESC.txt
inst/extdata/pwm/HUVEC.txt
inst/extdata/pwm/HeLa-S3.txt
inst/extdata/pwm/HepG2.txt
inst/extdata/pwm/K562.txt
inst/extdata/pwm/MCF7.txt
inst/extdata/pwm/NHEK.txt
inst/extdata/pwm/ProgFib.txt
man
man/ASN.Rd
man/Alphabet.Rd
man/DNA.Rd
man/RNA.Rd
man/createDiffLogoObject.Rd
man/diffLogo.Rd
man/diffLogoFromPwm.Rd
man/diffLogoTable.Rd
man/differenceOfICs.Rd
man/getPwmFromAlignment.Rd
man/informationContent.Rd
man/lossOfAbsICDifferences.Rd
man/normalizedDifferenceOfProbabilities.Rd
man/probabilities.Rd
man/seqLogo.Rd
man/shannonDivergence.Rd
man/sumOfAbsICDifferences.Rd
man/sumOfAbsProbabilityDifferences.Rd
man/sumProbabilities.Rd
scripts
scripts/DiffLogoExample.R
scripts/DiffLogo_dna_example.R
scripts/MotifDbTest.R
scripts/ctcf.R
scripts/ebox.R
scripts/fbox.R
tests
tests/testthat
tests/testthat.R
tests/testthat/test_baseDistributions.R
tests/testthat/test_stackHeights.R
tests/testthat/test_utilities.R
vignettes
vignettes/DiffLogoBasics.Rnw
DiffLogo documentation built on May 20, 2017, 10:40 p.m.