Files in GreenleafLab/chromVAR

Chromatin Variation Across Regions

R/AllClasses.R R/RcppExports.R R/background_peaks.R R/chromVAR.R R/cis.R R/clustering.R R/compute_deviations.R R/compute_variability.R R/differential_tests.R R/dimensionality_reduction.R R/filtering.R R/get_annotations.R R/get_inputs.R R/helper_functions.R R/kmers.R R/match_kmers.R R/motifs.R R/plotting.R R/pwm_dist.R R/test_sets.R R/utils.R R/variability_synergy.R README.md data-raw/example_counts.R man/addGCBias.Rd man/annotationMatches.Rd man/assembleKmers.Rd man/cbind-chromVARDeviations-method.Rd man/chromVAR.Rd man/chromVARDeviations-class.Rd man/chromVAR_theme.Rd man/computeDeviations.Rd man/computeExpectations.Rd man/computeVariability.Rd man/counts.Rd man/deviationScores.Rd man/deviations.Rd man/deviationsCovariability.Rd man/deviationsTsne.Rd man/differentialDeviations.Rd man/differentialVariability.Rd man/example_counts.Rd man/filterPeaks.Rd man/filterSamples.Rd man/filterSamplesPlot.Rd man/getAnnotationCorrelation.Rd man/getAnnotationSynergy.Rd man/getAnnotations.Rd man/getBackgroundPeaks.Rd man/getCisGroups.Rd man/getCounts.Rd man/getFragmentsPerPeak.Rd man/getFragmentsPerSample.Rd man/getJasparMotifs.Rd man/getPeaks.Rd man/getPermutedData.Rd man/getSampleCorrelation.Rd man/getSampleDepths.Rd man/getSampleDistance.Rd man/getTotalFragments.Rd man/makeBiasBins.Rd man/makePermutedSets.Rd man/matchKmers.Rd man/mini_counts.Rd man/mini_dev.Rd man/mini_ix.Rd man/plotDeviationsTsne.Rd man/plotKmerMismatch.Rd man/plotVariability.Rd man/pwmDistance.Rd man/rbind-chromVARDeviations-method.Rd man/readNarrowpeaks.Rd tests/testthat.R tests/testthat/test_compute_deviations.R tests/testthat/test_get_annotations.R tests/testthat/test_get_counts.R tests/testthat/test_peaks.R vignettes/Articles/Annotations.Rmd vignettes/Articles/Applications.Rmd vignettes/Articles/Counts.Rmd vignettes/Articles/Deviations.Rmd vignettes/Introduction.Rmd