descostesn/ChIPSeqSpike
ChIP-Seq data scaling according to spike-in control

Package index
Search the descostesn/ChIPSeqSpike package
Functions
244
Source code
16
Man pages
46
Home
/
GitHub
/
descostesn/ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control
/
API

API for descostesn/ChIPSeqSpike
ChIP-Seq data scaling according to spike-in control

Global functions
.callPlot Source code
.callRatio Source code
.checkInfoFile Source code
.checkPercentages Source code
.checkPlotHeatmapsParam Source code
.computeBamCount Source code
.computeScaling Source code
.computeScalingBoost Source code
.computeScalingFactor Source code
.convertTypes Source code
.loadCorrelationPlot Source code
.loadExtractionOnList Source code
.loadInputSubtractionList Source code
.loadOnList Source code
.loadScalingOnList Source code
.modifyBigWigName Source code
.notFoundMessage Source code
.perform_boxplot_violinplot Source code
.perform_heatscatterplot Source code
.plotAverageProfiles Source code
.plotLegends Source code
.plotSpiked Source code
.readInfoFile Source code
.removingNABigWig Source code
.retrieveAllFiles Source code
.retrieveAverageValuesList Source code
.retrieveIndexes Source code
.retrieveIndexesFromAllTypes Source code
.retrieveMatBindingList Source code
.retrieveMeanBindingValues Source code
.retrieveSF Source code
.subtractScores Source code
.summaryDatasetList Source code
.validateBigWig Source code
.validateMatBindingValList Source code
.validateParameters Source code
.validatePath Source code
.validatePlotSetArrayList Source code
.validateSFAndCount Source code
.verifyDataset Source code
ChIPSeqSpikeCore Man page Source code
ChIPSeqSpikeCore-class Man page
ChIPSeqSpikeDataset Man page Source code
ChIPSeqSpikeDataset-class Man page
ChIPSeqSpikeDatasetBoost Man page Source code
ChIPSeqSpikeDatasetBoost-class Man page
ChIPSeqSpikeDatasetList Man page Source code
ChIPSeqSpikeDatasetList-class Man page
ChIPSeqSpikeDatasetListBoost Man page Source code
ChIPSeqSpikeDatasetListBoost-class Man page
Experiment Man page Source code
Experiment-class Man page
ExperimentLoaded Man page Source code
ExperimentLoaded-class Man page
[[,ChIPSeqSpikeDataset,ANY,ANY-method Man page
[[,ChIPSeqSpikeDatasetList,ANY,ANY-method Man page
[[,ChIPSeqSpikeDatasetListBoost,ANY,ANY-method Man page
[[<-,ChIPSeqSpikeDataset,ANY,ANY-method Man page
[[<-,ChIPSeqSpikeDatasetList,ANY,ANY-method Man page
[[<-,Experiment,ANY,ANY-method Man page
averageBindingValues Man page
averageBindingValues<- Man page
averageBindingValues<-,ChIPSeqSpikeCore-method Man page
averageBindingValues<-,ChIPSeqSpikeDataset-method Man page
averageBindingValues<-,ChIPSeqSpikeDatasetBoost-method Man page
bigWigFile Man page
bigWigFile<- Man page
bigWigFile<-,ChIPSeqSpikeCore-method Man page
bigWigFile<-,ChIPSeqSpikeDataset-method Man page
bigWigFile<-,ChIPSeqSpikeDatasetBoost-method Man page
bigWigFile<-,Experiment-method Man page
bigWigFile<-,ExperimentLoaded-method Man page
boxplotSpike Man page
boxplotSpike,ChIPSeqSpikeDataset-method Man page
boxplotSpike,ChIPSeqSpikeDatasetBoost-method Man page
boxplotSpike,ChIPSeqSpikeDatasetList-method Man page
boxplotSpike,ChIPSeqSpikeDatasetListBoost-method Man page
count Man page
count<- Man page
count<-,ChIPSeqSpikeCore-method Man page
count<-,ChIPSeqSpikeDataset-method Man page
count<-,ChIPSeqSpikeDatasetBoost-method Man page
count<-,Experiment-method Man page
count<-,ExperimentLoaded-method Man page
csds Man page
datasetList Man page
datasetList<- Man page
datasetList<-,ChIPSeqSpikeDatasetList-method Man page
datasetList<-,ChIPSeqSpikeDatasetListBoost-method Man page
estimateScalingFactors Man page
estimateScalingFactors,ChIPSeqSpikeDataset-method Man page
estimateScalingFactors,ChIPSeqSpikeDatasetBoost-method Man page
estimateScalingFactors,ChIPSeqSpikeDatasetList-method Man page
estimateScalingFactors,ChIPSeqSpikeDatasetListBoost-method Man page
estimateScalingFactors,Experiment-method Man page
estimateScalingFactors,ExperimentLoaded-method Man page
exoCount Man page
exoCount<- Man page
exoCount<-,Experiment-method Man page
exoCount<-,ExperimentLoaded-method Man page
exogenousScalingFactor Man page
exogenousScalingFactor<- Man page
exogenousScalingFactor<-,Experiment-method Man page
exogenousScalingFactor<-,ExperimentLoaded-method Man page
experimentList Man page
experimentList<- Man page
experimentList<-,ChIPSeqSpikeDataset-method Man page
experimentList<-,ChIPSeqSpikeDatasetBoost-method Man page
exportBigWigs Man page
exportBigWigs,ChIPSeqSpikeDatasetBoost-method Man page
exportBigWigs,ChIPSeqSpikeDatasetListBoost-method Man page
extractBinding Man page
extractBinding,ChIPSeqSpikeDataset-method Man page
extractBinding,ChIPSeqSpikeDatasetBoost-method Man page
extractBinding,ChIPSeqSpikeDatasetList-method Man page
extractBinding,ChIPSeqSpikeDatasetListBoost-method Man page
getAverageBindingValues Man page
getAverageBindingValues,ChIPSeqSpikeCore-method Man page
getAverageBindingValues,ChIPSeqSpikeDataset-method Man page
getAverageBindingValues,ChIPSeqSpikeDatasetBoost-method Man page
getBam Man page
getBam,ChIPSeqSpikeCore-method Man page
getBam,ChIPSeqSpikeDataset-method Man page
getBam,ChIPSeqSpikeDatasetBoost-method Man page
getBam,Experiment-method Man page
getBam,ExperimentLoaded-method Man page
getBigWigFile Man page
getBigWigFile,ChIPSeqSpikeCore-method Man page
getBigWigFile,ChIPSeqSpikeDataset-method Man page
getBigWigFile,ChIPSeqSpikeDatasetBoost-method Man page
getBigWigFile,ChIPSeqSpikeDatasetList-method Man page
getBigWigFile,Experiment-method Man page
getBigWigFile,ExperimentLoaded-method Man page
getCount Man page
getCount,ChIPSeqSpikeCore-method Man page
getCount,ChIPSeqSpikeDataset-method Man page
getCount,ChIPSeqSpikeDatasetBoost-method Man page
getCount,Experiment-method Man page
getCount,ExperimentLoaded-method Man page
getDatasetList Man page
getDatasetList,ChIPSeqSpikeDatasetList-method Man page
getDatasetList,ChIPSeqSpikeDatasetListBoost-method Man page
getExoCount Man page
getExoCount,Experiment-method Man page
getExoCount,ExperimentLoaded-method Man page
getExogenousBam Man page
getExogenousBam,Experiment-method Man page
getExogenousBam,ExperimentLoaded-method Man page
getExogenousScalingFactor Man page
getExogenousScalingFactor,Experiment-method Man page
getExogenousScalingFactor,ExperimentLoaded-method Man page
getExpName Man page
getExpName,ChIPSeqSpikeDataset-method Man page
getExpName,ChIPSeqSpikeDatasetBoost-method Man page
getExpName,Experiment-method Man page
getExpName,ExperimentLoaded-method Man page
getExperimentList Man page
getExperimentList,ChIPSeqSpikeDataset-method Man page
getExperimentList,ChIPSeqSpikeDatasetBoost-method Man page
getExperimentListBigWigs Man page
getExperimentListBigWigs,ChIPSeqSpikeDataset-method Man page
getExperimentListBigWigs,ChIPSeqSpikeDatasetBoost-method Man page
getLoadedData Man page
getLoadedData,ChIPSeqSpikeDatasetBoost-method Man page
getLoadedData,ExperimentLoaded-method Man page
getMatBindingValues Man page
getMatBindingValues,ChIPSeqSpikeCore-method Man page
getMatBindingValues,ChIPSeqSpikeDataset-method Man page
getMatBindingValues,ChIPSeqSpikeDatasetBoost-method Man page
getRatio Man page
getRatio,ChIPSeqSpikeDataset-method Man page
getRatio,ChIPSeqSpikeDatasetBoost-method Man page
getRatio,ChIPSeqSpikeDatasetList-method Man page
getRatio,ChIPSeqSpikeDatasetListBoost-method Man page
getRatio,Experiment-method Man page
getRatio,ExperimentLoaded-method Man page
getScalingFactor Man page
getScalingFactor,ChIPSeqSpikeCore-method Man page
getScalingFactor,ChIPSeqSpikeDataset-method Man page
getScalingFactor,ChIPSeqSpikeDatasetBoost-method Man page
getScalingFactor,Experiment-method Man page
getScalingFactor,ExperimentLoaded-method Man page
inputSubtraction Man page
inputSubtraction,ChIPSeqSpikeDataset-method Man page
inputSubtraction,ChIPSeqSpikeDatasetBoost-method Man page
inputSubtraction,ChIPSeqSpikeDatasetList-method Man page
inputSubtraction,ChIPSeqSpikeDatasetListBoost-method Man page
matBindingValues Man page
matBindingValues<- Man page
matBindingValues<-,ChIPSeqSpikeCore-method Man page
matBindingValues<-,ChIPSeqSpikeDataset-method Man page
matBindingValues<-,ChIPSeqSpikeDatasetBoost-method Man page
plotCor Man page
plotCor,ChIPSeqSpikeDataset-method Man page
plotCor,ChIPSeqSpikeDatasetBoost-method Man page
plotCor,ChIPSeqSpikeDatasetList-method Man page
plotCor,ChIPSeqSpikeDatasetListBoost-method Man page
plotHeatmaps Man page
plotHeatmaps,ChIPSeqSpikeDataset-method Man page
plotHeatmaps,ChIPSeqSpikeDatasetBoost-method Man page
plotHeatmaps,ChIPSeqSpikeDatasetList-method Man page
plotHeatmaps,ChIPSeqSpikeDatasetListBoost-method Man page
plotProfile Man page
plotProfile,ChIPSeqSpikeDataset-method Man page
plotProfile,ChIPSeqSpikeDatasetBoost-method Man page
plotProfile,ChIPSeqSpikeDatasetList-method Man page
plotProfile,ChIPSeqSpikeDatasetListBoost-method Man page
plotTransform Man page
plotTransform,ChIPSeqSpikeDataset-method Man page
plotTransform,ChIPSeqSpikeDatasetList-method Man page
ratio Man page
result_data Man page
result_estimateScalingFactors Man page
result_extractBinding Man page
scaling Man page
scaling,ChIPSeqSpikeDataset-method Man page
scaling,ChIPSeqSpikeDatasetBoost-method Man page
scaling,ChIPSeqSpikeDatasetList-method Man page
scaling,ChIPSeqSpikeDatasetListBoost-method Man page
scalingFactor Man page
scalingFactor<- Man page
scalingFactor<-,ChIPSeqSpikeCore-method Man page
scalingFactor<-,ChIPSeqSpikeDataset-method Man page
scalingFactor<-,ChIPSeqSpikeDatasetBoost-method Man page
scalingFactor<-,Experiment-method Man page
scalingFactor<-,ExperimentLoaded-method Man page
spikeDataset Man page Source code
spikePipe Man page Source code
spikeSummary Man page
spikeSummary,ChIPSeqSpikeDataset-method Man page
spikeSummary,ChIPSeqSpikeDatasetBoost-method Man page
spikeSummary,ChIPSeqSpikeDatasetList-method Man page
spikeSummary,ChIPSeqSpikeDatasetListBoost-method Man page
spikeSummary,Experiment-method Man page
spikeSummary,ExperimentLoaded-method Man page
descostesn/ChIPSeqSpike documentation built on Aug. 6, 2019, 3:51 p.m.

R Package Documentation

rdrr.io home R language documentation Run R code online

Browse R Packages

CRAN packages Bioconductor packages R-Forge packages GitHub packages

We want your feedback!

Note that we can't provide technical support on individual packages. You should contact the package authors for that.
GitHub issue tracker
ian@mutexlabs.com
Personal blog

 
Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.

Close