Files in GreenleafLab/chromVAR
Chromatin Variation Across Regions
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
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
_pkgdown.yml
data-raw/example_counts.R
data/example_counts.rda
data/mini_counts.rda
data/mini_dev.rda
data/mini_ix.rda
inst/CITATION
inst/extdata/counts_table.tsv
inst/extdata/deviations_test
inst/extdata/test_RG.bam
inst/extdata/test_anno1.bed
inst/extdata/test_anno2.bed
inst/extdata/test_anno3.bed
inst/extdata/test_bed.txt
inst/extdata/test_reads.bed
inst/extdata/test_single1.bam
inst/extdata/test_single2.bam
inst/extdata/test_single3.bam
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
src/Makevars
src/RcppExports.cpp
src/pwm_similarity.cpp
src/utils.cpp
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
