Files in mgledi/DiffLogo
DiffLogo: A comparative visualisation of biooligomer motifs
.gitignore
DESCRIPTION
NAMESPACE
R/alphabet.R
R/baseDistrs.R
R/diffSeqLogo.R
R/diffSeqLogoSupport.R
R/preconditions.R
R/pwmAlignment.R
R/seqLogo.R
R/stackHeights.R
R/utilities.R
README.md
built/DiffLogo_0.99.0.tar.gz
built/DiffLogo_0.99.0_R_x86_64-unknown-linux-gnu.tar.gz
built/DiffLogo_0.99.1.tar.gz
built/DiffLogo_0.99.1_R_x86_64-unknown-linux-gnu.tar.gz
built/DiffLogo_0.99.2.tar.gz
built/DiffLogo_0.99.2_R_x86_64-unknown-linux-gnu.tar.gz
inst/CITATION
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/homer/CTCF_SatelliteElement_Zf_CD4.motif
inst/extdata/homer/CTCF_Zf_CD4.motif
inst/extdata/homer/Max.motif
inst/extdata/homer/c-Myc.motif
inst/extdata/pfm/ctcf_jaspar.pfm
inst/extdata/pwm/GM12878.pwm
inst/extdata/pwm/H1-hESC.pwm
inst/extdata/pwm/HUVEC.pwm
inst/extdata/pwm/HeLa-S3.pwm
inst/extdata/pwm/HepG2.pwm
inst/extdata/pwm/K562.pwm
inst/extdata/pwm/MCF7.pwm
inst/extdata/pwm/NHEK.pwm
inst/extdata/pwm/ProgFib.pwm
man/ASN.Rd
man/Alphabet.Rd
man/DNA.Rd
man/FULL_ALPHABET.Rd
man/RNA.Rd
man/alignPwmSets.Rd
man/baseDistributionPwm.Rd
man/calculatePvalue.Rd
man/createDiffLogoObject.Rd
man/diffLogo.Rd
man/diffLogoFromPwm.Rd
man/diffLogoTable.Rd
man/diffLogoTableConfiguration.Rd
man/differenceOfICs.Rd
man/drawDiffLogoTable.Rd
man/enrichDiffLogoObjectWithPvalues.Rd
man/enrichDiffLogoTableWithPvalues.Rd
man/extendPwmsFromAlignmentVector.Rd
man/getAlphabetFromCharacters.Rd
man/getAlphabetFromSequences.Rd
man/getPwmFromAlignment.Rd
man/getPwmFromAlignmentFile.Rd
man/getPwmFromFastaFile.Rd
man/getPwmFromFile.Rd
man/getPwmFromHomerFile.Rd
man/getPwmFromPfmOrJasparFile.Rd
man/getPwmFromPwmFile.Rd
man/getSequencesFromAlignmentFile.Rd
man/getSequencesFromFastaFile.Rd
man/informationContent.Rd
man/localPwmAlignment.Rd
man/lossOfAbsICDifferences.Rd
man/multipleLocalPwmsAlignment.Rd
man/normalizePWM.Rd
man/normalizedDifferenceOfProbabilities.Rd
man/prepareDiffLogoTable.Rd
man/probabilities.Rd
man/pwmDivergence.Rd
man/pwmsDistanceMatrix.Rd
man/reverseAlignmentVector.Rd
man/seqLogo.Rd
man/shannonDivergence.Rd
man/sumOfAbsICDifferences.Rd
man/sumOfAbsProbabilityDifferences.Rd
man/sumProbabilities.Rd
man/switchDirection.Rd
man/twoSetsAveragePwmDivergenceFromAlignmentVector.Rd
scripts/ctcf.R
scripts/ebox.R
scripts/fbox.R
tests/testthat.R
tests/testthat/test_alignment.R
tests/testthat/test_baseDistributions.R
tests/testthat/test_stackHeights.R
tests/testthat/test_utilities.R
vignettes/DiffLogoBasics.Rnw
