Files in gstricker/GenoGAM
A GAM based framework for analysis of ChIP-Seq data
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/Coordinates-class.R
R/GenoGAM-class.R
R/GenoGAM-package.R
R/GenoGAMDataSet-class.R
R/GenoGAMDataSetList-class.R
R/GenoGAMFamily-class.R
R/GenoGAMList-class.R
R/GenoGAMSettings-class.R
R/GenoGAMSetup-class.R
R/RcppExports.R
R/background.R
R/broadPeaks.R
R/cv.R
R/diffBinding.R
R/estimation.R
R/genogam.R
R/hdf5_handler.R
R/helper.R
R/misc.R
R/narrowPeaks.R
R/peakCalling.R
R/plotting.R
R/pvals.R
R/readData.R
R/sf.R
R/zzz.R
README.md
TODO.Rmd
inst/extdata/Set1/README
inst/extdata/Set1/bam/H3K4ME3_Full_length_Set1_Rep_1_chr1_100k.bam
inst/extdata/Set1/bam/H3K4ME3_Full_length_Set1_Rep_1_chr1_100k.bam.bai
inst/extdata/Set1/bam/H3K4ME3_Full_length_Set1_Rep_2_chr1_100k.bam
inst/extdata/Set1/bam/H3K4ME3_Full_length_Set1_Rep_2_chr1_100k.bam.bai
inst/extdata/Set1/bam/H3K4ME3_aa762-1080_Set1_Rep_1_chr1_100k.bam
inst/extdata/Set1/bam/H3K4ME3_aa762-1080_Set1_Rep_1_chr1_100k.bam.bai
inst/extdata/Set1/bam/H3K4ME3_aa762-1080_Set1_Rep_2_chr1_100k.bam
inst/extdata/Set1/bam/H3K4ME3_aa762-1080_Set1_Rep_2_chr1_100k.bam.bai
inst/extdata/Set1/experimentDesign.txt
man/Coordinates-class.Rd
man/GenoGAM-class.Rd
man/GenoGAM.Rd
man/GenoGAMDataSet-class.Rd
man/GenoGAMDataSet-metrics.Rd
man/GenoGAMDataSet-subsetting.Rd
man/GenoGAMDataSetList-class.Rd
man/GenoGAMDataSetList-metrics.Rd
man/GenoGAMDataSetList-subsetting.Rd
man/GenoGAMFamily-class.Rd
man/GenoGAMList-class.Rd
man/GenoGAMList-subsetting.Rd
man/GenoGAMSettings-class.Rd
man/asCoordinates.Rd
man/callPeaks.Rd
man/computeRegionSignificance.Rd
man/computeSignificance.Rd
man/computeSizeFactors.Rd
man/fitGenoGAM.Rd
man/makeTestGenoGAM.Rd
man/makeTestGenoGAMDataSet.Rd
man/makeTestGenoGAMDataSetList.Rd
man/makeTestGenoGAMList.Rd
man/plotGenoGAM.Rd
man/readData.Rd
man/writeToBEDFile.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/matrixMult.cpp
tests/testthat.R
tests/testthat/.Rhistory
tests/testthat/test_GenoGAM-class.R
tests/testthat/test_GenoGAMDataSet.R
tests/testthat/test_GenoGAMDataSetList.R
tests/testthat/test_GenoGAMList-class.R
tests/testthat/test_GenoGAMSettings-class.R
tests/testthat/test_GenoGAMSetup-class.R
tests/testthat/test_bugs.R
tests/testthat/test_cv.R
tests/testthat/test_filter.R
tests/testthat/test_genogam.R
tests/testthat/test_helper.R
tests/testthat/test_sizeFactors.R
vignettes/GenoGAM.Rmd
vignettes/bibliog.bib
vignettes/img/overview.png
vignettes/img/splines.png
