Files in steveped/chipExtra

Additional functions for working with ChIP-Seq data

.BBSoptions

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/AllGenerics.R R/aaa.R R/addDiffStatus.R R/asTibble.R R/bestOverlap.R R/chopMC.R R/colToRanges.R R/collapseGenes.R R/data.R R/defineRegions.R R/defineSeqinfo.R R/distinctMC.R R/dualFilter.R R/extraChIPs.R R/fitAssayDiff.R R/getProfileData.R R/grlToSE.R R/importPeaks.R R/makeConsensus.R R/mapByFeature.R R/mapGrlCols.R R/mergeByCol.R R/mergeByHMP.R R/mergeBySig.R R/partitionRanges.R R/plotAssayDensities.R R/plotAssayHeatmap.R R/plotAssayPCA.R R/plotAssayRle.R R/plotGrlCol.R R/plotHFGC.R R/plotOverlaps.R R/plotPairwise.R R/plotPie.R R/plotProfileHeatmap.R R/plotSplitDonut.R R/propOverlaps.R R/reduceMC.R R/setoptsMC.R R/stitchRanges.R R/voomWeightsFromCPM.R README.md

_pkgdown.yml

data-raw/sticker.R

data/ex_genes.rda

data/ex_hic.rda

data/ex_prom.rda

data/ex_trans.rda

data/grch37.cytobands.rda

data/grch38.cytobands.rda

data/peaks.rda

data/se.rda

inst/extdata/ER_1.narrowPeak

inst/extdata/ER_2.narrowPeak

inst/extdata/bam/ex1.bam

inst/extdata/bam/ex1.bam.bai

inst/extdata/bam/ex2.bam

inst/extdata/bam/ex2.bam.bai

inst/extdata/bam/input.bam

inst/extdata/bam/input.bam.bai

inst/extdata/bigwig/ex1.bw

inst/extdata/bigwig/ex2.bw

inst/extdata/peaks.bed.gz

inst/extdata/testFiles/test.broadPeak

inst/extdata/testFiles/test.narrowPeak

inst/references.bib

inst/script/datasets.R inst/script/ex_datasets.md longtests/testthat.R longtests/testthat/test_dualFilter.R longtests/testthat/test_getProfileData.R longtests/testthat/test_mapping.R longtests/testthat/test_plotHFGC.R man/addDiffStatus-methods.Rd man/as_tibble.Rd man/bestOverlap-methods.Rd man/chopMC.Rd man/colToRanges-methods.Rd man/collapseGenes.Rd man/cytobands.Rd man/defineRegions.Rd man/defineSeqinfo.Rd man/distinctMC.Rd man/dot-makeFinalProfileHeatmap.Rd man/dot-mapFeatures.Rd man/dot-mapGi.Rd man/dot-mapWithin.Rd man/dualFilter.Rd man/ex_datasets.Rd man/extraChIPs-package.Rd

man/figures/extraChIPs.png

man/figures/extraChips_noText.png

man/figures/favicon.png

man/fitAssayDiff-methods.Rd man/fixed_width_datasets.Rd man/getProfileData-methods.Rd man/grlToSE-methods.Rd man/importPeaks.Rd man/makeConsensus.Rd man/mapByFeature.Rd man/mapGrlCols.Rd man/mergeByCol-methods.Rd man/mergeByHMP-methods.Rd man/mergeBySig-methods.Rd man/partitionRanges-methods.Rd man/plotAssayDensities-methods.Rd man/plotAssayHeatmap-methods.Rd man/plotAssayPCA-methods.Rd man/plotAssayRle-methods.Rd man/plotGrlCol.Rd man/plotHFGC.Rd man/plotOverlaps-methods.Rd man/plotPairwise.Rd man/plotPie-methods.Rd man/plotProfileHeatmap-methods.Rd man/plotSplitDonut-methods.Rd man/propOverlap-methods.Rd man/reduceMC.Rd man/setoptsMC-methods.Rd man/stitchRanges.Rd man/voomWeightsFromCPM.Rd

src/FMStable.c

src/init.c

tests/testthat.R tests/testthat/test_addDiffStatus.R tests/testthat/test_bestOverlap.R tests/testthat/test_chopMC.R tests/testthat/test_colToRanges.R tests/testthat/test_collapseGenes.R tests/testthat/test_defineRegions.R tests/testthat/test_defineSeqinfo.R tests/testthat/test_distinctMC.R tests/testthat/test_fitAssayDiff.R tests/testthat/test_getProfileData.R tests/testthat/test_grlToSE.R tests/testthat/test_importPeaks.R tests/testthat/test_makeConsensus.R tests/testthat/test_mapGrlCols.R tests/testthat/test_mapping.R tests/testthat/test_mergeByCol.R tests/testthat/test_mergeByHMP.R tests/testthat/test_mergeBySig.R tests/testthat/test_overlapsProp.R tests/testthat/test_partitionRanges.R tests/testthat/test_plotAssays.R tests/testthat/test_plotGrlCol.R tests/testthat/test_plotHFGC.R tests/testthat/test_plotOverlaps.R tests/testthat/test_plotPairwise.R tests/testthat/test_plotPie.R tests/testthat/test_plotProfileHeatmap.R tests/testthat/test_plotSplitDonut.R tests/testthat/test_setoptsMC.R tests/testthat/test_stitchRanges.R tests/testthat/test_tibbleConversion.R tests/testthat/test_voomWeightsFromCPM.R vignettes/differential_signal_fixed.Rmd vignettes/differential_signal_sliding.Rmd

vignettes/differential_signal_sliding_files/figure-gfm/compare-logfc-tmm-cqn-1.png

vignettes/differential_signal_sliding_files/figure-gfm/cqn-1.png

vignettes/differential_signal_sliding_files/figure-gfm/gc-bias-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-assay-rle-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-bias-cqn-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-cqn-pca-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-densities-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-density-pca-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-donut-both-palettes-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-donut-customised-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-donut-default-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-hfgc-cov-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-hfgc-init-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-hfgc-with-annot-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-hfgc-with-genes-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-hfgc-with-regions-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-ma-libsize-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-ma-mapped-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-ma-tmm-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-pca-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-pie-generic-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-pie-labels-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-pie-width-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plot-width-logcpm-1.png

vignettes/differential_signal_sliding_files/figure-gfm/plotcpm-1.png

vignettes/range_based_functions.Rmd

vignettes/stitched.png

steveped/chipExtra documentation built on May 2, 2024, 12:11 p.m.