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
