Files in databio/GenomicDistributions
GenomicDistributions: fast analysis of genomic intervals with Bioconductor
.Rbuildignore
.github/.gitignore
.github/workflows/lint.yml
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/aggregate.R
R/buildReferenceData.R
R/chrom-plots.R
R/content-plots.R
R/data.R
R/feature-plots.R
R/loadData.R
R/neighbor-distances.R
R/package.R
R/partition-plots.R
R/qthist.R
R/specificity-plots.R
R/utility.R
R/zalias.R
README.md
_pkgdown.yaml
data-raw/TSS_hg19.R
data-raw/bedfiles.R
data-raw/chromSizes_hg19.R
data-raw/geneModels_hg19.R
data/TSS_hg19.rda
data/cellTypeMetadata.rda
data/chromSizes_hg19.rda
data/datalist
data/exampleOpenSignalMatrix_hg19.rda
data/geneModels_hg19.rda
data/setB_100.rda
data/vistaEnhancers.rda
inst/CITATION
inst/extdata/C_elegans_cropped_example.fa.gz
inst/extdata/C_elegans_cropped_example.gtf.gz
inst/extdata/example_cell_matrix.txt
inst/extdata/setB_100.bed.gz
inst/extdata/vistaEnhancers.bed.gz
long_vignettes/full-power.Rmd
long_vignettes/render-long-vignettes.R
man/BSdtToGRanges.Rd
man/GenomicDistributions.Rd
man/TSS_hg19.Rd
man/binBSGenome.Rd
man/binChroms.Rd
man/binRegion.Rd
man/calcChromBins.Rd
man/calcChromBinsRef.Rd
man/calcChromBinsRefSlow.Rd
man/calcCumulativePartitions.Rd
man/calcCumulativePartitionsRef.Rd
man/calcDinuclFreq.Rd
man/calcDinuclFreqRef.Rd
man/calcExpectedPartitions.Rd
man/calcExpectedPartitionsRef.Rd
man/calcFeatureDist.Rd
man/calcFeatureDistRefTSS.Rd
man/calcGCContent.Rd
man/calcGCContentRef.Rd
man/calcNearestNeighbors.Rd
man/calcNeighborDist.Rd
man/calcPartitions.Rd
man/calcPartitionsRef.Rd
man/calcSummarySignal.Rd
man/calcWidth.Rd
man/cellTypeMetadata.Rd
man/chromSizes_hg19.Rd
man/dot-requireAndReturn.Rd
man/dot-validateInputs.Rd
man/dtToGr.Rd
man/dtToGrInternal.Rd
man/exampleOpenSignalMatrix_hg19.Rd
man/geneModels_hg19.Rd
man/genomePartitionList.Rd
man/getChromSizes.Rd
man/getChromSizesFromFasta.Rd
man/getGeneModels.Rd
man/getGeneModelsFromGTF.Rd
man/getGenomeBins.Rd
man/getReferenceData.Rd
man/getTssFromGTF.Rd
man/grToDt.Rd
man/labelCuts.Rd
man/loadBSgenome.Rd
man/loadEnsDb.Rd
man/neighbordt.Rd
man/nlist.Rd
man/plotChromBins.Rd
man/plotCumulativePartitions.Rd
man/plotDinuclFreq.Rd
man/plotExpectedPartitions.Rd
man/plotFeatureDist.Rd
man/plotGCContent.Rd
man/plotNeighborDist.Rd
man/plotPartitions.Rd
man/plotQTHist.Rd
man/plotSummarySignal.Rd
man/retrieveFile.Rd
man/setB_100.Rd
man/splitDataTable.Rd
man/theme_blank_facet_label.Rd
man/vistaEnhancers.Rd
tests/testthat.R
tests/testthat/testChrom.R
tests/testthat/testGCContent.R
tests/testthat/testNeighborDist.R
tests/testthat/testOpenChromatin.R
tests/testthat/testPartitions.R
tests/testthat/test_all.R
vignettes/figures-full-power/GC-content-1.png
vignettes/figures-full-power/TSS-plot-1.png
vignettes/figures-full-power/TSS-plot-closeup-1.png
vignettes/figures-full-power/chrom-bin-plot-1.png
vignettes/figures-full-power/cumulative-partitions-1.png
vignettes/figures-full-power/custom-cumulative-partitions-1.png
vignettes/figures-full-power/custom-expected-partition-plot-1.png
vignettes/figures-full-power/custom-partition-plot-1.png
vignettes/figures-full-power/dinuc-content-1.png
vignettes/figures-full-power/expected-partition-plot-1.png
vignettes/figures-full-power/gene-distance-plot-1.png
vignettes/figures-full-power/neighbor-distance-distribution-1.png
vignettes/figures-full-power/open-signal-1.png
vignettes/figures-full-power/partition-plot-1.png
vignettes/figures-full-power/partition-plot-proportional-1.png
vignettes/figures-full-power/width-distribution-1.png
vignettes/full-power.Rmd
vignettes/intro.Rmd
