Files in descostesn/ChIPSeqSpike
ChIP-Seq data scaling according to spike-in control
.project
DESCRIPTION
NAMESPACE
NEWS
R/AllClasses.R
R/AllGenerics.R
R/accessor-methods.R
R/constructors.R
R/estimateScalingFactors-methods.R
R/extractBinding-methods.R
R/inputSubtraction-methods.R
R/plot-methods.R
R/replace-methods.R
R/scaling-methods.R
R/spikePipe-methods.R
data/ratio.RData
data/result_estimateScalingFactors.RData
data/result_extractBinding.RData
inst/doc/ChIPSeqSpike.pdf
inst/extdata/bam_files/H3K79me2_0_dm3-filtered.bam
inst/extdata/bam_files/H3K79me2_0_hg19-filtered.bam
inst/extdata/bam_files/H3K79me2_100_dm3-filtered.bam
inst/extdata/bam_files/H3K79me2_100_hg19-filtered.bam
inst/extdata/bam_files/H3K79me2_50_dm3-filtered.bam
inst/extdata/bam_files/H3K79me2_50_hg19-filtered.bam
inst/extdata/bam_files/input_0_hg19-filtered.bam
inst/extdata/bam_files/input_100_hg19-filtered.bam
inst/extdata/bam_files/input_50_hg19-filtered.bam
inst/extdata/bigwig_files/H3K79me2_0-filtered.bw
inst/extdata/bigwig_files/H3K79me2_100-filtered.bw
inst/extdata/bigwig_files/H3K79me2_50-filtered.bw
inst/extdata/bigwig_files/input_0-filtered.bw
inst/extdata/bigwig_files/input_100-filtered.bw
inst/extdata/bigwig_files/input_50-filtered.bw
inst/extdata/empty_files/endoBam_empty.bam
inst/extdata/empty_files/exoBam_empty.bam
inst/extdata/empty_files/input.wig_empty.bw
inst/extdata/empty_files/inputwig_empty.bw
inst/extdata/empty_files/inputwig_empty.wig
inst/extdata/empty_files/wig.file_empty.bw
inst/extdata/empty_files/wigfile_empty-RPM.bw
inst/extdata/empty_files/wigfile_empty.bw
inst/extdata/fastq_fasta_files/endo.fa
inst/extdata/fastq_fasta_files/exo.fa
inst/extdata/fastq_fasta_files/reads1.fastq.gz
inst/extdata/fastq_fasta_files/reads2.fastq.gz
inst/extdata/info.csv
inst/extdata/test_coord.gff
man/ChIPSeqSpikeCore.Rd
man/ChIPSeqSpikeDataset-class.Rd
man/ChIPSeqSpikeDatasetBoost-class.Rd
man/ChIPSeqSpikeDatasetList-class.Rd
man/ChIPSeqSpikeDatasetListBoost-class.Rd
man/Experiment-class.Rd
man/ExperimentLoaded-class.Rd
man/averageBindingValues.Rd
man/bigWigFile.Rd
man/boxplotSpike.Rd
man/count.Rd
man/datasetList.Rd
man/estimateScalingFactors.Rd
man/exoCount.Rd
man/exogenousScalingFactor.Rd
man/experimentList.Rd
man/exportBigWigs.Rd
man/extractBinding.Rd
man/getAverageBindingValues.Rd
man/getBam.Rd
man/getBigWigFile.Rd
man/getCount.Rd
man/getDatasetList.Rd
man/getExoCount.Rd
man/getExogenousBam.Rd
man/getExogenousScalingFactor.Rd
man/getExpName.Rd
man/getExperimentList.Rd
man/getExperimentListBigWigs.Rd
man/getLoadedData.Rd
man/getMatBindingValues.Rd
man/getRatio.Rd
man/getScalingFactor.Rd
man/inputSubtraction.Rd
man/matBindingValues.Rd
man/plotCor.Rd
man/plotHeatmaps.Rd
man/plotProfile.Rd
man/plotTransform.Rd
man/ratio.Rd
man/result_data.Rd
man/scaling.Rd
man/scalingFactor.Rd
man/spikeDataset.Rd
man/spikePipe.Rd
man/spikeSummary.Rd
tests/testthat.R
tests/testthat/test-functions.R
tests/testthat/test-getters.R
tests/testthat/test-objectsCreation.R
tests/testthat/test-setters.R
vignettes/.Rhistory
vignettes/ChIPSeqSpike.Rmd
vignettes/cor_log.pdf
vignettes/heatmaps_start-2.png
