DiffLogo: DiffLogo: A comparative visualisation of sequence motifs

Share:

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

Author
Martin Nettling [aut], Hendrik Treutler [aut, cre], Jan Grau [aut, ctb], Jens Keilwagen [aut, ctb], Stefan Posch [aut], Ivo Grosse [aut]
Date of publication
None
Maintainer
Hendrik Treutler <htreutle@ipb-halle.de>
License
GPL (>= 2)
Version
1.4.0
URLs

View on Bioconductor

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

Files in this package

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