Package: DiffLogo 2.37.0

Hendrik Treutler

DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

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

Authors:c, person, person, person, person, person, person)

DiffLogo_2.37.0.tar.gz
DiffLogo_2.37.0.zip(r-4.7)DiffLogo_2.37.0.zip(r-4.6)DiffLogo_2.37.0.zip(r-4.5)
DiffLogo_2.37.0.tgz(r-4.6-any)DiffLogo_2.37.0.tgz(r-4.5-any)
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DiffLogo_2.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
DiffLogo/json (API)

# Install 'DiffLogo' in R:

install.packages('DiffLogo', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mgledi/difflogo/issues

On BioConductor:DiffLogo-2.37.0(bioc 3.24)DiffLogo-2.36.0(bioc 3.23)

software sequencematching multiplecomparison motifannotation visualization alignment

6.86 score 7 stars 49 scripts 7 mentions 40 exports 2 dependencies

Last updated from:7b72497ee1. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	151
linux-devel-x86_64	WARNING	167
source / vignettes	OK	238
linux-release-x86_64	WARNING	213
macos-release-arm64	WARNING	80
macos-oldrel-arm64	WARNING	86
windows-devel	WARNING	137
windows-release	WARNING	94
windows-oldrel	WARNING	101
wasm-release	OK	123

Exports:Alphabet ASN calculatePvalue createDiffLogoObject differenceOfICs diffLogo diffLogoFromPwm diffLogoTable diffLogoTableConfiguration DNA drawDiffLogoTable enrichDiffLogoObjectWithPvalues enrichDiffLogoTableWithPvalues extendPwmsFromAlignmentVector FULL_ALPHABET getAlphabetFromCharacters getAlphabetFromSequences getPwmFromAlignment getPwmFromAlignmentFile getPwmFromFastaFile getPwmFromFile getPwmFromHomerFile getPwmFromPfmOrJasparFile getPwmFromPwmFile getSequencesFromAlignmentFile getSequencesFromFastaFile informationContent lossOfAbsICDifferences multipleLocalPwmsAlignment normalizedDifferenceOfProbabilities normalizePWM prepareDiffLogoTable probabilities pwmDivergence RNA seqLogo shannonDivergence sumOfAbsICDifferences sumOfAbsProbabilityDifferences sumProbabilities

Dependencies:cba proxy

Basics of the DiffLogo package

Rendered fromDiffLogoBasics.Rnwusingutils::Sweave

Last update: 2017-07-07
Started: 2015-09-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Multiple PWMs alignment	alignPwmSets
built alphabet	Alphabet
ASN alphabet	ASN
Generates a PWM	baseDistributionPwm
p-value that two PWM-positions are from the same distribution	calculatePvalue
DiffLogo object	createDiffLogoObject
normalized information content differences	differenceOfICs
Draw DiffLogo	diffLogo
Draw DiffLogo from PWM	diffLogoFromPwm
Draw DiffLogo-table	diffLogoTable
Configuration object for diffLogoTable	diffLogoTableConfiguration
DNA alphabet	DNA
Draws a table of DiffLogos	drawDiffLogoTable
Enriches a difflogo object with p-values	enrichDiffLogoObjectWithPvalues
Enriches a matrix of difflogo objects with p-values	enrichDiffLogoTableWithPvalues
Extend pwms with respect to alignment	extendPwmsFromAlignmentVector
Complete character alphabet	FULL_ALPHABET
returns the alphabet which fits to the given characters	getAlphabetFromCharacters
returns the alphabet which fits to the given sequences	getAlphabetFromSequences
Create PWM from alignment	getPwmFromAlignment
generates a pwm from an alignment file	getPwmFromAlignmentFile
generates a pwm from a FASTA file	getPwmFromFastaFile
generates a pwm from a file of different formats	getPwmFromFile
generates a pwm from a homer file	getPwmFromHomerFile
generates a pwm from a jaspar file	getPwmFromPfmOrJasparFile
generates a pwm from a pwm file	getPwmFromPwmFile
extracts the sequences from an alignment file	getSequencesFromAlignmentFile
extracts the sequences from a FASTA file	getSequencesFromFastaFile
information content	informationContent
Align pwms	localPwmAlignment
the change of information content	lossOfAbsICDifferences
Multiple PWMs alignment	multipleLocalPwmsAlignment
normalized probability differences	normalizedDifferenceOfProbabilities
normalizes the given pwm	normalizePWM
Prepare a table of difflogo objects	prepareDiffLogoTable
probabilities	probabilities
PWM divergence	pwmDivergence
Multiple PWMs alignment	pwmsDistanceMatrix
Reverse for alignment vector	reverseAlignmentVector
RNA alphabet	RNA
Draw sequence logo	seqLogo
shannon divergence	shannonDivergence
sum of absolute information content differences	sumOfAbsICDifferences
sum of absolute probability differences	sumOfAbsProbabilityDifferences
sum of probabilities, i.e. 1.0	sumProbabilities
Switches between 'forward' and 'reverse'	switchDirection
Average divergence between two sets.	twoSetsAveragePwmDivergenceFromAlignmentVector