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

Share:

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.

Author
Benedikt Zacher, Johannes Soeding, Pei Fen Kuan, Matthias Siebert, Achim Tresch
Date of publication
None
Maintainer
Benedikt Zacher <zacher@lmb.uni-muenchen.de>
License
Artistic-2.0
Version
1.30.0

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

Files in this package

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