├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── AllClasses.R ├── RcppExports.R ├── background_peaks.R ├── chromVAR.R ├── cis.R ├── clustering.R ├── compute_deviations.R ├── compute_variability.R ├── differential_tests.R ├── dimensionality_reduction.R ├── filtering.R ├── get_annotations.R ├── get_inputs.R ├── helper_functions.R ├── kmers.R ├── match_kmers.R ├── motifs.R ├── plotting.R ├── pwm_dist.R ├── test_sets.R ├── utils.R └── variability_synergy.R ├── README.md ├── _pkgdown.yml ├── data-raw └── example_counts.R ├── data ├── example_counts.rda ├── mini_counts.rda ├── mini_dev.rda └── mini_ix.rda ├── inst ├── CITATION └── extdata │ ├── counts_table.tsv │ ├── deviations_test │ ├── test_RG.bam │ ├── test_anno1.bed │ ├── test_anno2.bed │ ├── test_anno3.bed │ ├── test_bed.txt │ ├── test_reads.bed │ ├── test_single1.bam │ ├── test_single2.bam │ └── test_single3.bam ├── man ├── addGCBias.Rd ├── annotationMatches.Rd ├── assembleKmers.Rd ├── cbind-chromVARDeviations-method.Rd ├── chromVAR.Rd ├── chromVARDeviations-class.Rd ├── chromVAR_theme.Rd ├── computeDeviations.Rd ├── computeExpectations.Rd ├── computeVariability.Rd ├── counts.Rd ├── deviationScores.Rd ├── deviations.Rd ├── deviationsCovariability.Rd ├── deviationsTsne.Rd ├── differentialDeviations.Rd ├── differentialVariability.Rd ├── example_counts.Rd ├── filterPeaks.Rd ├── filterSamples.Rd ├── filterSamplesPlot.Rd ├── getAnnotationCorrelation.Rd ├── getAnnotationSynergy.Rd ├── getAnnotations.Rd ├── getBackgroundPeaks.Rd ├── getCisGroups.Rd ├── getCounts.Rd ├── getFragmentsPerPeak.Rd ├── getFragmentsPerSample.Rd ├── getJasparMotifs.Rd ├── getPeaks.Rd ├── getPermutedData.Rd ├── getSampleCorrelation.Rd ├── getSampleDepths.Rd ├── getSampleDistance.Rd ├── getTotalFragments.Rd ├── makeBiasBins.Rd ├── makePermutedSets.Rd ├── matchKmers.Rd ├── mini_counts.Rd ├── mini_dev.Rd ├── mini_ix.Rd ├── plotDeviationsTsne.Rd ├── plotKmerMismatch.Rd ├── plotVariability.Rd ├── pwmDistance.Rd ├── rbind-chromVARDeviations-method.Rd └── readNarrowpeaks.Rd ├── src ├── Makevars ├── RcppExports.cpp ├── pwm_similarity.cpp └── utils.cpp ├── tests ├── testthat.R └── testthat │ ├── test_compute_deviations.R │ ├── test_get_annotations.R │ ├── test_get_counts.R │ └── test_peaks.R └── vignettes ├── Articles ├── Annotations.Rmd ├── Applications.Rmd ├── Counts.Rmd └── Deviations.Rmd └── Introduction.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GreenleafLab/chromVAR/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GreenleafLab/chromVAR/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: 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