Files in UMI4Cats
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

NEWS
NAMESPACE
DESCRIPTION
README.md tests/testthat.R tests/testthat/test-UMI4Cclass.R tests/testthat/test-contactsUMI4C.R tests/testthat/test-downloadUMI4Cexample.R tests/testthat/test-digestGenome.R tests/testthat/test-getViewpointCoordinates.R tests/testthat/test-statsUMI4C.R tests/testthat/test-createGeneAnnotation.R R/getViewpointCoordinates.R R/AllClasses.R R/UMI4Cats.R R/AllGenerics.R R/utils-pipe.R R/groupUMI4C.R R/analyzeUMI4C.R R/AllMethods.R R/differentialFisherUMI4C.R R/statsUMI4C.R R/plotUMI4C.R R/contactsUMI4C.R R/differentialNbinomWaldTestUMI4C.R R/digestGenome.R R/demultiplexFastq.R R/createGeneAnnotation.R R/downloadUMI4CexampleData.R man/digestGenome.Rd man/counterUMI4C.Rd man/UMI4C-methods.Rd man/alignmentUMI4C.Rd man/plotUMI4C.Rd man/getNormalizationMatrix.Rd man/getFactors.Rd man/pipe.Rd man/demultiplexFastq.Rd man/downloadUMI4CexampleData.Rd man/UMI4C2dds.Rd man/dot-getSummaryBam.Rd man/UMI4Cats.Rd man/dot-smoothMonotone.Rd man/addGrouping.Rd man/dot-singleSplitUMI4C.Rd man/dot-singleAlignmentUMI4C.Rd man/darken.Rd man/formatPlotsUMI4C.Rd man/UMI4C.Rd man/geoMeanCoordinates.Rd man/fisherUMI4C.Rd man/splitUMI4C.Rd man/differentialNbinomWaldTestUMI4C.Rd man/nbinomWaldTestUMI4C.Rd man/contactsUMI4C.Rd man/getViewpointCoordinates.Rd man/themeYblank.Rd man/groupSamplesUMI4C.Rd man/ex_ciita_umi4c.Rd man/createStatsTable.Rd man/plotGenes.Rd man/addStepping.Rd man/calculateDomainogram.Rd man/statsUMI4C.Rd man/dot-singleCounterUMI4C.Rd man/smoothMonotoneUMI4C.Rd man/themeXblank.Rd man/themeXYblank.Rd man/vstUMI4C.Rd man/dot-getCache.Rd man/prepUMI4C.Rd man/calculateAdaptativeTrend.Rd man/plotTrend.Rd man/getColors.Rd man/plotDomainogram.Rd man/dot-singlePrepUMI4C.Rd man/deseq2UMI4C.Rd man/plotDifferential.Rd man/createGeneAnnotation.Rd man/theme.Rd
man/figures/README-unnamed-chunk-5-2.png
man/figures/README-analysis-plot-2.png
man/figures/logo.png
man/figures/UMI4Cats.png
man/figures/README-analysis-plot-1.png
man/figures/UMI4Cats.svg
man/figures/README-unnamed-chunk-5-1.png
inst/CITATION
inst/extdata/CIITA/logs/umi4c_stats.txt
inst/extdata/CIITA/logs/stats_summary.txt
inst/extdata/CIITA/logs/umi4c_alignment_stats.txt
inst/extdata/CIITA/count/cyt_hi32_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/ctrl_hi24_CIITA_counts.tsv.gz
inst/doc/UMI4Cats.html
inst/doc/UMI4Cats.Rmd inst/doc/UMI4Cats.R inst/scripts/CIITA_process_example.R inst/scripts/CIITA_generate_reduced_fastq.R
data/ex_ciita_umi4c.rda
data/datalist
build/vignette.rds
vignettes/UMI4Cats.Rmd
vignettes/bibliography.bib
vignettes/figures/scheme.svg
vignettes/figures/logo.png
vignettes/figures/differentialNbinomWaldTestUMI4C.svg
vignettes/figures/scheme.png
vignettes/figures/read_scheme.svg
vignettes/figures/read_scheme.png
vignettes/figures/differentialNbinomWaldTestUMI4C.png
UMI4Cats documentation built on Dec. 31, 2020, 2:01 a.m.