gstricker/fastGenoGAM
A GAM based framework for analysis of ChIP-Seq data

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Search the gstricker/fastGenoGAM package
Vignettes
Functions
165
Source code
38
Man pages
26
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gstricker/fastGenoGAM: A GAM based framework for analysis of ChIP-Seq data
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API

API for gstricker/fastGenoGAM
A GAM based framework for analysis of ChIP-Seq data

Global functions
Coordinates Man page
Coordinates-class Man page
GenoGAM Man page
GenoGAM-class Man page
GenoGAMDataSet Man page
GenoGAMDataSet-class Man page
GenoGAMDataSetList Man page
GenoGAMDataSetList-class Man page
GenoGAMFamily-class Man page
GenoGAMList Man page
GenoGAMList-class Man page
GenoGAMSettings Man page
GenoGAMSettings-class Man page
IQR,GenoGAMDataSet-method Man page
IQR,GenoGAMDataSetList-method Man page
Summary,GenoGAMDataSet-method Man page
Summary,GenoGAMDataSetList-method Man page
[,GenoGAM,GRanges,ANY,ANY-method Man page
[,GenoGAMDataSet,GRanges,ANY,ANY-method Man page
[,GenoGAMDataSetList,GRanges,ANY,ANY-method Man page
[,GenoGAMList,GRanges,ANY,ANY-method Man page
asCoordinates Man page
assay,GenoGAM,missing-method Man page
assay,GenoGAMDataSetList,ANY-method Man page
assay,GenoGAMList,missing-method Man page
assays,GenoGAMDataSetList-method Man page
assays,GenoGAMList-method Man page
callPeaks Man page
colData Man page
colData,GenoGAM-method Man page
colData,GenoGAMDataSetList-method Man page
colData,GenoGAMList-method Man page
colnames Man page
colnames,GenoGAM-method Man page
colnames,GenoGAMDataSetList-method Man page
colnames,GenoGAMList-method Man page
computeRegionSignificance Man page
computeSignificance Man page
computeSizeFactors Man page
dataRange Man page
dataRange,GenoGAMDataSet-method Man page
dataRange,GenoGAMDataSetList-method Man page
design,GenoGAM-method Man page
design,GenoGAMDataSet-method Man page
design,GenoGAMDataSetList-method Man page
design,GenoGAMList-method Man page
design<-,GenoGAMDataSet,ANY-method Man page
design<-,GenoGAMDataSetList,ANY-method Man page
dim,GenoGAMDataSetList-method Man page
dim,GenoGAMList-method Man page
dimnames Man page
dimnames,GenoGAM-method Man page
dimnames,GenoGAMList-method Man page
end,Coordinates-method Man page
end<-,Coordinates-method Man page
fastGenoGAM Man page
fastGenoGAM-package Man page
fits Man page
fits,GenoGAM-method Man page
fits,GenoGAMList-method Man page
genogam Man page
getChromosomes Man page
getChromosomes,GenoGAMDataSet-method Man page
getChromosomes,GenoGAMDataSetList-method Man page
getChunkSize Man page
getChunkSize,GenoGAMDataSet-method Man page
getChunkSize,GenoGAMDataSetList-method Man page
getChunkSize<- Man page
getChunkSize<-,GenoGAMDataSet,numeric-method Man page
getChunkSize<-,GenoGAMDataSetList,numeric-method Man page
getCoefs Man page
getCoefs,GenoGAM-method Man page
getCoefs,GenoGAMList-method Man page
getCountMatrix,GenoGAMDataSet-method Man page
getCountMatrix,GenoGAMDataSetList-method Man page
getFamily Man page
getFamily,GenoGAM-method Man page
getFamily,GenoGAMList-method Man page
getIndex Man page
getIndex,GenoGAMDataSet-method Man page
getIndex,GenoGAMDataSetList-method Man page
getKnots Man page
getKnots,GenoGAM-method Man page
getKnots,GenoGAMList-method Man page
getOverhangSize Man page
getOverhangSize,GenoGAMDataSet-method Man page
getOverhangSize,GenoGAMDataSetList-method Man page
getOverhangSize<- Man page
getOverhangSize<-,GenoGAMDataSet,numeric-method Man page
getOverhangSize<-,GenoGAMDataSetList,numeric-method Man page
getParams Man page
getParams,GenoGAM-method Man page
getParams,GenoGAMList-method Man page
getSettings Man page
getSettings,GenoGAM-method Man page
getSettings,GenoGAMList-method Man page
getTileNumber Man page
getTileNumber,GenoGAMDataSet-method Man page
getTileNumber,GenoGAMDataSetList-method Man page
getTileNumber<- Man page
getTileNumber<-,GenoGAMDataSet,numeric-method Man page
getTileNumber<-,GenoGAMDataSetList,numeric-method Man page
getTileSize Man page
getTileSize,GenoGAMDataSet-method Man page
getTileSize,GenoGAMDataSetList-method Man page
getTileSize<- Man page
getTileSize<-,GenoGAMDataSet,numeric-method Man page
getTileSize<-,GenoGAMDataSetList,numeric-method Man page
is.HDF5,GenoGAM-method Man page
is.HDF5,GenoGAMDataSet-method Man page
is.HDF5,GenoGAMDataSetList-method Man page
is.HDF5,GenoGAMList-method Man page
length,Coordinates-method Man page
length,GenoGAMDataSetList-method Man page
length,GenoGAMList-method Man page
mad,GenoGAMDataSet-method Man page
mad,GenoGAMDataSetList-method Man page
makeTestGenoGAM Man page
makeTestGenoGAMDataSet Man page
makeTestGenoGAMDataSetList Man page
makeTestGenoGAMList Man page
mean,GenoGAMDataSet-method Man page
mean,GenoGAMDataSetList-method Man page
median,GenoGAMDataSet-method Man page
median,GenoGAMDataSetList-method Man page
ncol,Coordinates-method Man page
nrow,Coordinates-method Man page
plotGenoGAM Man page
pvalue,GenoGAM-method Man page
pvalue,GenoGAMList-method Man page
readData Man page
rowRanges,GenoGAMDataSetList-method Man page
rowRanges,GenoGAMList-method Man page
sd,GenoGAMDataSet-method Man page
sd,GenoGAMDataSetList-method Man page
se Man page
se,GenoGAM-method Man page
se,GenoGAMList-method Man page
seqlengths,GenoGAMDataSetList-method Man page
seqlengths,GenoGAMList-method Man page
seqlevels,GenoGAMDataSetList-method Man page
seqlevels,GenoGAMList-method Man page
seqlevelsInUse,GenoGAMDataSetList-method Man page
seqlevelsInUse,GenoGAMList-method Man page
sizeFactors,GenoGAM-method Man page
sizeFactors,GenoGAMDataSet-method Man page
sizeFactors,GenoGAMDataSetList-method Man page
sizeFactors,GenoGAMList-method Man page
sizeFactors<-,GenoGAMDataSet,ANY-method Man page
sizeFactors<-,GenoGAMDataSetList,ANY-method Man page
start,Coordinates-method Man page
start<-,Coordinates-method Man page
subset,GenoGAMDataSet-method Man page
subset,GenoGAMDataSetList-method Man page
subset,GenoGAMList-method Man page
subsetByOverlaps,GenoGAMDataSet,GRanges-method Man page
subsetByOverlaps,GenoGAMDataSetList,GRanges-method Man page
subsetByOverlaps,GenoGAMList,GRanges-method Man page
tileSettings Man page
tileSettings,GenoGAMDataSet-method Man page
tileSettings,GenoGAMDataSetList-method Man page
var,GenoGAMDataSet,ANY-method Man page
var,GenoGAMDataSetList,ANY-method Man page
width,Coordinates-method Man page
writeToBEDFile Man page
gstricker/fastGenoGAM documentation built on May 17, 2019, 8:56 a.m.

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