Files in Pasquali-lab/UMI4Cats
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
.Rbuildignore
.github/.gitignore
.github/CODE_OF_CONDUCT.md
.github/CONTRIBUTING.md
.github/ISSUE_TEMPLATE/issue_template.md
.github/SUPPORT.md
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/AllClasses.R
R/AllGenerics.R
R/AllMethods.R
R/UMI4Cats.R
R/analyzeUMI4C.R
R/callInteractions.R
R/contactsUMI4C.R
R/createGeneAnnotation.R
R/demultiplexFastq.R
R/differentialFisherUMI4C.R
R/differentialNbinomWaldTestUMI4C.R
R/digestGenome.R
R/downloadUMI4CexampleData.R
R/getViewpointCoordinates.R
R/groupUMI4C.R
R/plotUMI4C.R
R/statsUMI4C.R
R/utils-pipe.R
R/utils.R
R/waldUMI4C.R
README.md
data/ex_ciita_umi4c.rda
inst/CITATION
inst/extdata/CIITA/count/ctrl_hi24_CIITA_counts.tsv.gz
inst/extdata/CIITA/count/ctrl_hi32_CIITA_counts.tsv.gz
inst/extdata/CIITA/count/cyt_hi24_CIITA_counts.tsv.gz
inst/extdata/CIITA/count/cyt_hi32_CIITA_counts.tsv.gz
inst/extdata/CIITA/logs/stats_summary.txt
inst/extdata/CIITA/logs/umi4c_alignment_stats.txt
inst/extdata/CIITA/logs/umi4c_stats.txt
inst/scripts/CIITA_generate_reduced_fastq.R
inst/scripts/CIITA_process_example.R
man/UMI4C-methods.Rd
man/UMI4C.Rd
man/UMI4C2dds.Rd
man/UMI4Cats.Rd
man/addGrouping.Rd
man/addStepping.Rd
man/alignmentUMI4C.Rd
man/calculateAdaptativeTrend.Rd
man/calculateDomainogram.Rd
man/callInteractions.Rd
man/combineUMI4C.Rd
man/contactsUMI4C.Rd
man/counterUMI4C.Rd
man/createGeneAnnotation.Rd
man/createStatsTable.Rd
man/darken.Rd
man/dds2UMI4C.Rd
man/demultiplexFastq.Rd
man/differentialNbinomWaldTestUMI4C.Rd
man/digestGenome.Rd
man/dot-getCache.Rd
man/dot-getSummaryBam.Rd
man/dot-singleAlignmentUMI4C.Rd
man/dot-singleCounterUMI4C.Rd
man/dot-singlePrepUMI4C.Rd
man/dot-singleSplitUMI4C.Rd
man/dot-smoothMonotone.Rd
man/downloadUMI4CexampleData.Rd
man/ex_ciita_umi4c.Rd
man/figures/README-analysis-plot-1.png
man/figures/README-analysis-plot-2.png
man/figures/README-unnamed-chunk-5-1.png
man/figures/README-unnamed-chunk-5-2.png
man/figures/UMI4Cats.png
man/figures/UMI4Cats.svg
man/figures/logo.png
man/fisherUMI4C.Rd
man/formatPlotsUMI4C.Rd
man/geoMeanCoordinates.Rd
man/getColors.Rd
man/getFactors.Rd
man/getNormalizationMatrix.Rd
man/getSignInteractions.Rd
man/getViewpointCoordinates.Rd
man/groupSamplesUMI4C.Rd
man/makeWindowFragments.Rd
man/nbinomWaldTestUMI4C.Rd
man/pipe.Rd
man/plotDifferential.Rd
man/plotDomainogram.Rd
man/plotGenes.Rd
man/plotInteractions.Rd
man/plotInteractionsUMI4C.Rd
man/plotTrend.Rd
man/plotUMI4C.Rd
man/prepUMI4C.Rd
man/smoothMonotoneUMI4C.Rd
man/splitUMI4C.Rd
man/statsUMI4C.Rd
man/theme.Rd
man/themeXYblank.Rd
man/themeXblank.Rd
man/themeYblank.Rd
man/vstUMI4C.Rd
man/waldUMI4C.Rd
man/zscoreUMI4C.Rd
tests/testthat.R
tests/testthat/test-UMI4Cclass.R
tests/testthat/test-contactsUMI4C.R
tests/testthat/test-createGeneAnnotation.R
tests/testthat/test-digestGenome.R
tests/testthat/test-downloadUMI4Cexample.R
tests/testthat/test-getViewpointCoordinates.R
tests/testthat/test-statsUMI4C.R
vignettes/UMI4Cats.Rmd
vignettes/bibliography.bib
vignettes/figures/differentialNbinomWaldTestUMI4C.png
vignettes/figures/differentialNbinomWaldTestUMI4C.svg
vignettes/figures/logo.png
vignettes/figures/read_scheme.png
vignettes/figures/read_scheme.svg
vignettes/figures/scheme.png
vignettes/figures/scheme.svg
