Files in DiffLogo

DiffLogo: A comparative visualisation of biooligomer motifs

README.md

NAMESPACE

DESCRIPTION

build/vignette.rds

R/alphabet.R R/seqLogo.R R/pwmAlignment.R R/diffSeqLogoSupport.R R/utilities.R R/diffSeqLogo.R R/preconditions.R R/stackHeights.R R/baseDistrs.R

vignettes/DiffLogoBasics.Rnw

man/getAlphabetFromSequences.Rd man/drawDiffLogoTable.Rd man/getSequencesFromFastaFile.Rd man/getPwmFromFastaFile.Rd man/reverseAlignmentVector.Rd man/getSequencesFromAlignmentFile.Rd man/diffLogoTableConfiguration.Rd man/DNA.Rd man/probabilities.Rd man/diffLogoFromPwm.Rd man/calculatePvalue.Rd man/enrichDiffLogoObjectWithPvalues.Rd man/alignPwmSets.Rd man/localPwmAlignment.Rd man/differenceOfICs.Rd man/multipleLocalPwmsAlignment.Rd man/sumOfAbsICDifferences.Rd man/RNA.Rd man/twoSetsAveragePwmDivergenceFromAlignmentVector.Rd man/getPwmFromPfmOrJasparFile.Rd man/prepareDiffLogoTable.Rd man/seqLogo.Rd man/sumOfAbsProbabilityDifferences.Rd man/getAlphabetFromCharacters.Rd man/pwmDivergence.Rd man/shannonDivergence.Rd man/getPwmFromAlignmentFile.Rd man/enrichDiffLogoTableWithPvalues.Rd man/diffLogo.Rd man/extendPwmsFromAlignmentVector.Rd man/baseDistributionPwm.Rd man/createDiffLogoObject.Rd man/getPwmFromFile.Rd man/normalizedDifferenceOfProbabilities.Rd man/switchDirection.Rd man/Alphabet.Rd man/FULL_ALPHABET.Rd man/getPwmFromHomerFile.Rd man/ASN.Rd man/normalizePWM.Rd man/lossOfAbsICDifferences.Rd man/getPwmFromAlignment.Rd man/pwmsDistanceMatrix.Rd man/getPwmFromPwmFile.Rd man/sumProbabilities.Rd man/informationContent.Rd man/diffLogoTable.Rd tests/testthat.R tests/testthat/test_baseDistributions.R tests/testthat/test_stackHeights.R tests/testthat/test_alignment.R tests/testthat/test_utilities.R

inst/CITATION

inst/doc/DiffLogoBasics.Rnw

inst/doc/DiffLogoBasics.pdf inst/doc/DiffLogoBasics.R

inst/extdata/homer/c-Myc.motif

inst/extdata/homer/CTCF_SatelliteElement_Zf_CD4.motif

inst/extdata/homer/CTCF_Zf_CD4.motif

inst/extdata/homer/Max.motif

inst/extdata/pwm/ProgFib.pwm

inst/extdata/pwm/GM12878.pwm

inst/extdata/pwm/MCF7.pwm

inst/extdata/pwm/H1-hESC.pwm

inst/extdata/pwm/NHEK.pwm

inst/extdata/pwm/HUVEC.pwm

inst/extdata/pwm/K562.pwm

inst/extdata/pwm/HeLa-S3.pwm

inst/extdata/pwm/HepG2.pwm

inst/extdata/pfm/ctcf_jaspar.pfm

inst/extdata/alignments/Mad.txt

inst/extdata/alignments/calamodulin_2.txt

inst/extdata/alignments/ubiquitination_2.txt

inst/extdata/alignments/phosphorylation_1.txt

inst/extdata/alignments/F-box_metazoa.seq.fa

inst/extdata/alignments/Myc.txt

inst/extdata/alignments/F-box_fungi.seq.fa

inst/extdata/alignments/F-box_viridiplantae.seq.fa

inst/extdata/alignments/calamodulin_1.txt

inst/extdata/alignments/Max.txt

inst/extdata/alignments/F-box_bacteria.seq.fa

inst/extdata/alignments/ubiquitination_1.txt

inst/extdata/alignments/phosphorylation_2.txt

DiffLogo documentation built on Nov. 8, 2020, 6:09 p.m.