# Normalization and difference calling in ChIP-seq data

## Documentation for package ‘normr’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

normR-package | Enrichment, Difference and Regime Calling in ChIP-seq data.
BamsignalsConfig | Container for configuration of read counting with bamsignals in normR
BamsignalsCountConfig | Container for configuration of read counting with bamsignals in normR
configPairedEnd | Container for configuration of read counting with bamsignals in normR
configSingleEnd | Container for configuration of read counting with bamsignals in normR
countConfigPairedEnd | Container for configuration of read counting with bamsignals in normR
countConfigPairedEnd-method | Container for configuration of read counting with bamsignals in normR
countConfigSingleEnd | Container for configuration of read counting with bamsignals in normR
countConfigSingleEnd-method | Container for configuration of read counting with bamsignals in normR
differenceCall | Difference Calling between conditional ChIP-seq data in normR with diffR
DifferenceCalling | Difference Calling between conditional ChIP-seq data in normR with diffR
DifferentialPeakCalling | Enrichment, Difference and Regime Calling in ChIP-seq data.
diffR | Difference Calling between conditional ChIP-seq data in normR with diffR
diffr | Difference Calling between conditional ChIP-seq data in normR with diffR
diffR-generic | Difference Calling between conditional ChIP-seq data in normR with diffR
diffR-method | Difference Calling between conditional ChIP-seq data in normR with diffR
enrichmentCall | Enrichment Calling on ChIP-seq data in normR with enrichR
EnrichmentCalling | Enrichment Calling on ChIP-seq data in normR with enrichR
enrichR | Enrichment Calling on ChIP-seq data in normR with enrichR
enrichr | Enrichment Calling on ChIP-seq data in normR with enrichR
enrichR-generic | Enrichment Calling on ChIP-seq data in normR with enrichR
enrichR-method | Enrichment Calling on ChIP-seq data in normR with enrichR
exportR | Container for a fit done with normR
exportR-method | Container for a fit done with normR
getBamsignalsFilter | Container for configuration of read counting with bamsignals in normR
getClasses | Container for a fit done with normR
getClasses-method | Container for a fit done with normR
getCounts | Container for a fit done with normR
getCounts-method | Container for a fit done with normR
getEnrichment | Container for a fit done with normR
getEnrichment-method | Container for a fit done with normR
getFilter | Container for configuration of read counting with bamsignals in normR
getFilter-method | Container for configuration of read counting with bamsignals in normR
getNormRCountConfigFilter | Container for configuration of read counting with bamsignals in normR
getPosteriors | Container for a fit done with normR
getPosteriors-method | Container for a fit done with normR
getPvalues | Container for a fit done with normR
getPvalues-method | Container for a fit done with normR
getQvalues | Container for a fit done with normR
getQvalues-method | Container for a fit done with normR
getRanges | Container for a fit done with normR
getRanges-method | Container for a fit done with normR
length-method | Container for a fit done with normR
normR | Enrichment, Difference and Regime Calling in ChIP-seq data.
normr | Enrichment, Difference and Regime Calling in ChIP-seq data.
NormRCountConfig | Container for configuration of read counting with bamsignals in normR
NormRCountConfig-class | Container for configuration of read counting with bamsignals in normR
NormRFit | Container for a fit done with normR
NormRfit | Container for a fit done with normR
normRFit | Container for a fit done with normR
normrfit | Container for a fit done with normR
NormRFit-class | Container for a fit done with normR
PeakCalling | Enrichment, Difference and Regime Calling in ChIP-seq data.
plot-method | Container for a fit done with normR
plot.NormRFit | Container for a fit done with normR
print-method | Container for configuration of read counting with bamsignals in normR
print-method | Container for a fit done with normR
regimeCall | Regime Enrichment Calling for ChIP-seq data in normR with regimeR
RegimeCalling | Regime Enrichment Calling for ChIP-seq data in normR with regimeR
regimeR | Regime Enrichment Calling for ChIP-seq data in normR with regimeR
regimer | Regime Enrichment Calling for ChIP-seq data in normR with regimeR
regimeR-generic | Regime Enrichment Calling for ChIP-seq data in normR with regimeR
regimeR-method | Regime Enrichment Calling for ChIP-seq data in normR with regimeR
show-method | Container for configuration of read counting with bamsignals in normR
show-method | Container for a fit done with normR
summary-method | Container for a fit done with normR