Files in sjessa/chromswitch

An R package to detect chromatin state switches from epigenomic data

.Rbuildignore

.gitignore

.travis.yml

CONDUCT.md

DESCRIPTION

LICENSE

NAMESPACE

R/LocalPeaks-class.R R/binary_matrix.R R/chromswitch.R R/clustering.R R/coordinates.R R/data.R R/external_cluster_validity.R R/global_processing.R R/internal_cluster_validity.R R/local_processing.R R/read.R R/summary_matrix.R R/wrappers.R README.md

chromswitch.Rproj

data-raw/E068_H3K4me3_chr19.nPk.bed

data-raw/E071_H3K4me3_chr19.nPk.bed

data-raw/E074_H3K4me3_chr19.nPk.bed

data-raw/E101_H3K4me3_chr19.nPk.bed

data-raw/E102_H3K4me3_chr19.nPk.bed

data-raw/E110_H3K4me3_chr19.nPk.bed

data-raw/prep_raw.R

data/H3K4me3.rda

inst/CITATION

inst/NEWS

inst/extdata/E068.H3K4me3.bed

inst/extdata/E071.H3K4me3.bed

inst/extdata/E074.H3K4me3.bed

inst/extdata/E101.H3K4me3.bed

inst/extdata/E102.H3K4me3.bed

inst/extdata/E110.H3K4me3.bed

inst/extdata/metadata.tsv

inst/extdata/query.bed

man/GRangesToCoord.Rd man/H3K4me3.Rd man/LocalPeaks-class.Rd man/NMI.Rd man/binarizePeaks.Rd man/callBinary.Rd man/callSummary.Rd man/chromswitch.Rd man/classEntropy.Rd man/cluster.Rd man/clusterEntropy.Rd man/completeness.Rd man/conditionalClassEntropy.Rd man/conditionalClusterEntropy.Rd man/coordToGRanges.Rd man/filterPeaks.Rd man/homogeneity.Rd man/makeBrowserCoord.Rd man/normalizePeaks.Rd man/pReciprocalOverlap.Rd man/purity.Rd man/readNarrowPeak.Rd man/reducePeaks.Rd man/retrievePeaks.Rd man/summarizePeaks.Rd man/vMeasure.Rd man/winsorNorm.Rd

tests/test_data/basic.bed

tests/test_data/basic2.bed

tests/test_data/twocol.bed

tests/test_data/with_metadata.bed

tests/testthat.R tests/testthat/test-binary.R tests/testthat/test-cluster.R tests/testthat/test-coordinates.R tests/testthat/test-external_indices.R tests/testthat/test-global.R tests/testthat/test-internal_indices.R tests/testthat/test-local.R tests/testthat/test-localPeaks.R tests/testthat/test-read.R tests/testthat/test-summary.R tests/testthat/test-wrappers.R vignettes/chromswitch_intro.Rmd

vignettes/figures/flowchart.png

vignettes/figures/igv_screenshot.png

vignettes/figures/reduce.png

vignettes/figures/ttyh1_summary.png

sjessa/chromswitch documentation built on Feb. 4, 2024, 2:04 a.m.