Starr: Simple tiling array analysis of Affymetrix ChIP-chip data

Starr facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling arrays. The package provides functions for data import, quality assessment, data visualization and exploration. Furthermore, it includes high-level analysis features like association of ChIP signals with annotated features, correlation analysis of ChIP signals and other genomic data (e.g. gene expression), peak-finding with the CMARRT algorithm and comparative display of multiple clusters of ChIP-profiles. It uses the basic Bioconductor classes ExpressionSet and probeAnno for maximum compatibility with other software on Bioconductor. All functions from Starr can be used to investigate preprocessed data from the Ringo package, and vice versa. An important novel tool is the the automated generation of correct, up-to-date microarray probe annotation (bpmap) files, which relies on an efficient mapping of short sequences (e.g. the probe sequences on a microarray) to an arbitrary genome.

AuthorBenedikt Zacher, Johannes Soeding, Pei Fen Kuan, Matthias Siebert, Achim Tresch
Date of publicationNone
MaintainerBenedikt Zacher <zacher@lmb.uni-muenchen.de>
LicenseArtistic-2.0
Version1.30.0

View on Bioconductor

Man pages

backgd.sd: Background parameters (internal function)

bpmapToProbeAnno: Creating a probeAnno object

cmarrt.ma: Compute moving average statistics by incorporating the...

cmarrt.peak: Obtain bound regions for a given error rate control

correlate: Correlate the values of two named vectors

correlationPlot: correlation of ChIP signals to other data

declare.bound: Declare bound probes for a given error rate control

densityscatter: Compute density of a scatterplot

expressionByFeature: Getting expression value by feature from an ExpressionSet

fill: Fill large spaces in one profile with NA

fillNA: Fill large spaces in profiles with NA

filterGenes: Filter Features/Genes

getFeatures: Getting profiles of one annotated features with a given...

getIntensites: Get profile of anntated features from a probe mapping

getMeans: Get mean ChIP-signal over annotated features

getProfiles: Get profiles of ChIP-signal over annotated features

getProfilesByBase: Get profiles of ChIP-signal over annotated features...

getRatio: Building ratio over experiments

heatmapplot: heatmapplot

intersection: Get the intersection of two named vectors

kde2dplot: Compute density of a scatterplot

list2matrix: Convert profile list to matrix

makeProbeAnno: Creating a probeAnno object

makeSplines: Fit splines to profiles

mapFeatures: Map middle positions of probes to annotated features

ma.stat: Compute moving average statistics and p-values

match_ac: Exact String matching using the Aho-Corasick algorithm

normalize.Probes: Normalization of probes

plot.boxes: boxplots of experiments

plot.cmarrt: Histogram of p-values and normal QQ plots for standardized MA...

plot.Density: density plots of experiments

plot.gcBias: Visualize GC-Bias of Hybridization

plot.image: Reconstruct the array image

plot.ma: M versus A plot

plot.posBias: Bias of hybridzation, depending on base position in sequence.

plotProfiles: Plotting ChIP profiles of one or more clusters

plot.ratioScatter: Plot ratios of all possible combinations of IP and CONTROL

plot.scatter: High level scatterplot of experiments

profileplot: Vizualize clusters

rankPercentile.normalize: Rank precentile Normalization

readCelFile: Read raw intensities from CEL files

read.gffAnno: Reading gff annotation

remap: Remap reporter sequences to the genome and create a new bpmap...

RGlist2ExpressionSet: Convert an RGlist to an ExpressionSet

rm.small.peak: Remove bound regions which consist of too few probes

sameLength: Make equal length of upstream and downstream regions in a...

singleclusterplot: single cluster plot

sort.by.genomic: Pre-process the data by genomic location

substract: Substract mean or median from data

whichIn: Map positions to intervals

windowxy: Get mfcol or mfrow for a number of plots to one device

writeGFF: write ChIP-chip data to a gff file

writePosFile: Creating a pos file

writeWIG: write ChIP-chip data to a *.wig file

Functions

backgd.sd Man page
bpmapToProbeAnno Man page
cmarrt.ma Man page
cmarrt.peak Man page
correlate Man page
correlationPlot Man page
declare.bound Man page
densityscatter Man page
expressionByFeature Man page
fill Man page
fillNA Man page
filterGenes Man page
getFeature Man page
getIntensities Man page
getMeans Man page
getProfiles Man page
getProfilesByBase Man page
getRatio Man page
heatmapplot Man page
intersection Man page
kde2dplot Man page
list2matrix Man page
makeProbeAnno Man page
makeSplines Man page
mapFeatures Man page
ma.stat Man page
match_ac Man page
normalize.Probes Man page
plotBoxes Man page
plotcmarrt Man page
plotDensity Man page
plotGCbias Man page
plotImage Man page
plotMA Man page
plotPosBias Man page
plotProfiles Man page
plotRatioScatter Man page
plotScatter Man page
profileplot Man page
rankPercentile.normalize Man page
readCelFile Man page
read.gffAnno Man page
remap Man page
RGlist2ExpresionSet Man page
rm.small.peak Man page
sameLength Man page
singleclusterplot Man page
sortbygenomic Man page
substract Man page
whichIn Man page
windowxy Man page
writeGFF Man page
writePosFile Man page
writeWIG Man page

Files

Starr/DESCRIPTION
Starr/NAMESPACE
Starr/R
Starr/R/AhoCorasick.R Starr/R/Normalization.R Starr/R/RGlist2ExpresionSet.R Starr/R/backgd.sd.R Starr/R/cmarrt.ma.R Starr/R/cmarrt.peak.R Starr/R/correlationPlot.R Starr/R/declare.bound.R Starr/R/geneExpression.R Starr/R/getProfiles.R Starr/R/getProfilesByBase.R Starr/R/getProfilesMiddle.R Starr/R/heatmapplot.R Starr/R/list2matrix.R Starr/R/ma.stat.R Starr/R/makeProbeAnno.R Starr/R/makeSplines.R Starr/R/parseGffAnnotation.R Starr/R/plot.cmarrt.R Starr/R/plotProfiles.R Starr/R/profileplot.R Starr/R/quality_control.R Starr/R/readCelFile.R Starr/R/rm.small.peak.R Starr/R/sort.by.genomic.R Starr/R/whichIn.R Starr/R/writeGFF.R Starr/R/writeWIG.R
Starr/build
Starr/build/vignette.rds
Starr/configure
Starr/configure.in
Starr/inst
Starr/inst/doc
Starr/inst/doc/Starr.R
Starr/inst/doc/Starr.Rnw
Starr/inst/doc/Starr.pdf
Starr/inst/extdata
Starr/inst/extdata/Rpb3_IP2_chr1.cel
Starr/inst/extdata/Rpb3_IP_chr1.cel
Starr/inst/extdata/Scerevisiae_tlg_chr1.bpmap
Starr/inst/extdata/chrI.fa
Starr/inst/extdata/transcriptAnno.gff
Starr/inst/extdata/wt_IP_chr1.cel
Starr/man
Starr/man/RGlist2ExpressionSet.Rd Starr/man/backgd.sd.Rd Starr/man/bpmapToProbeAnno.Rd Starr/man/cmarrt.ma.Rd Starr/man/cmarrt.peak.Rd Starr/man/correlate.Rd Starr/man/correlationPlot.Rd Starr/man/declare.bound.Rd Starr/man/densityscatter.Rd Starr/man/expressionByFeature.Rd Starr/man/fill.Rd Starr/man/fillNA.Rd Starr/man/filterGenes.Rd Starr/man/getFeatures.Rd Starr/man/getIntensites.Rd Starr/man/getMeans.Rd Starr/man/getProfiles.Rd Starr/man/getProfilesByBase.Rd Starr/man/getRatio.Rd Starr/man/heatmapplot.Rd Starr/man/intersection.Rd Starr/man/kde2dplot.Rd Starr/man/list2matrix.Rd Starr/man/ma.stat.Rd Starr/man/makeProbeAnno.Rd Starr/man/makeSplines.Rd Starr/man/mapFeatures.Rd Starr/man/match_ac.Rd Starr/man/normalize.Probes.Rd Starr/man/plot.Density.Rd Starr/man/plot.boxes.Rd Starr/man/plot.cmarrt.Rd Starr/man/plot.gcBias.Rd Starr/man/plot.image.Rd Starr/man/plot.ma.Rd Starr/man/plot.posBias.Rd Starr/man/plot.ratioScatter.Rd Starr/man/plot.scatter.Rd Starr/man/plotProfiles.Rd Starr/man/profileplot.Rd Starr/man/rankPercentile.normalize.Rd Starr/man/read.gffAnno.Rd Starr/man/readCelFile.Rd Starr/man/remap.Rd Starr/man/rm.small.peak.Rd Starr/man/sameLength.Rd Starr/man/singleclusterplot.Rd Starr/man/sort.by.genomic.Rd Starr/man/substract.Rd Starr/man/whichIn.Rd Starr/man/windowxy.Rd Starr/man/writeGFF.Rd Starr/man/writePosFile.Rd Starr/man/writeWIG.Rd
Starr/src
Starr/src/Makevars
Starr/src/Makevars.in
Starr/src/Makevars.win
Starr/src/ahocorasick.c
Starr/src/collect.c
Starr/src/collect.h
Starr/src/fixed_gen_dist2.h
Starr/src/kseq.h
Starr/src/rm_small_peak.c
Starr/src/rm_small_peak.h
Starr/src/sort_by_genomic.c
Starr/src/sort_by_genomic.h
Starr/vignettes
Starr/vignettes/Starr.Rnw
Starr/vignettes/bibliography.bib

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