Package: DiffLogo 2.31.0

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_2.31.0.tar.gz
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DiffLogo.pdf |DiffLogo.html✨
DiffLogo/json (API)

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

Peer review:

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

On BioConductor:DiffLogo-2.31.0(bioc 3.21)DiffLogo-2.30.0(bioc 3.20)

softwaresequencematchingmultiplecomparisonmotifannotationvisualizationalignment

6.66 score 8 stars 27 scripts 208 downloads 7 mentions 40 exports 2 dependencies

Last updated 2 months agofrom:33af0b4ebd. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winWARNINGNov 29 2024
R-4.5-linuxWARNINGNov 29 2024
R-4.4-winWARNINGNov 29 2024
R-4.4-macWARNINGNov 29 2024
R-4.3-winWARNINGNov 29 2024
R-4.3-macWARNINGNov 29 2024

Exports:AlphabetASNcalculatePvaluecreateDiffLogoObjectdifferenceOfICsdiffLogodiffLogoFromPwmdiffLogoTablediffLogoTableConfigurationDNAdrawDiffLogoTableenrichDiffLogoObjectWithPvaluesenrichDiffLogoTableWithPvaluesextendPwmsFromAlignmentVectorFULL_ALPHABETgetAlphabetFromCharactersgetAlphabetFromSequencesgetPwmFromAlignmentgetPwmFromAlignmentFilegetPwmFromFastaFilegetPwmFromFilegetPwmFromHomerFilegetPwmFromPfmOrJasparFilegetPwmFromPwmFilegetSequencesFromAlignmentFilegetSequencesFromFastaFileinformationContentlossOfAbsICDifferencesmultipleLocalPwmsAlignmentnormalizedDifferenceOfProbabilitiesnormalizePWMprepareDiffLogoTableprobabilitiespwmDivergenceRNAseqLogoshannonDivergencesumOfAbsICDifferencessumOfAbsProbabilityDifferencessumProbabilities

Dependencies:cbaproxy

Basics of the DiffLogo package

Rendered fromDiffLogoBasics.Rnwusingutils::Sweaveon Nov 29 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Multiple PWMs alignmentalignPwmSets
built alphabetAlphabet
ASN alphabetASN
Generates a PWMbaseDistributionPwm
p-value that two PWM-positions are from the same distributioncalculatePvalue
DiffLogo objectcreateDiffLogoObject
normalized information content differencesdifferenceOfICs
Draw DiffLogodiffLogo
Draw DiffLogo from PWMdiffLogoFromPwm
Draw DiffLogo-tablediffLogoTable
Configuration object for diffLogoTablediffLogoTableConfiguration
DNA alphabetDNA
Draws a table of DiffLogosdrawDiffLogoTable
Enriches a difflogo object with p-valuesenrichDiffLogoObjectWithPvalues
Enriches a matrix of difflogo objects with p-valuesenrichDiffLogoTableWithPvalues
Extend pwms with respect to alignmentextendPwmsFromAlignmentVector
Complete character alphabetFULL_ALPHABET
returns the alphabet which fits to the given charactersgetAlphabetFromCharacters
returns the alphabet which fits to the given sequencesgetAlphabetFromSequences
Create PWM from alignmentgetPwmFromAlignment
generates a pwm from an alignment filegetPwmFromAlignmentFile
generates a pwm from a FASTA filegetPwmFromFastaFile
generates a pwm from a file of different formatsgetPwmFromFile
generates a pwm from a homer filegetPwmFromHomerFile
generates a pwm from a jaspar filegetPwmFromPfmOrJasparFile
generates a pwm from a pwm filegetPwmFromPwmFile
extracts the sequences from an alignment filegetSequencesFromAlignmentFile
extracts the sequences from a FASTA filegetSequencesFromFastaFile
information contentinformationContent
Align pwmslocalPwmAlignment
the change of information contentlossOfAbsICDifferences
Multiple PWMs alignmentmultipleLocalPwmsAlignment
normalized probability differencesnormalizedDifferenceOfProbabilities
normalizes the given pwmnormalizePWM
Prepare a table of difflogo objectsprepareDiffLogoTable
probabilitiesprobabilities
PWM divergencepwmDivergence
Multiple PWMs alignmentpwmsDistanceMatrix
Reverse for alignment vectorreverseAlignmentVector
RNA alphabetRNA
Draw sequence logoseqLogo
shannon divergenceshannonDivergence
sum of absolute information content differencessumOfAbsICDifferences
sum of absolute probability differencessumOfAbsProbabilityDifferences
sum of probabilities, i.e. 1.0sumProbabilities
Switches between 'forward' and 'reverse'switchDirection
Average divergence between two sets.twoSetsAveragePwmDivergenceFromAlignmentVector