Starr

Package: Starr
Version: 1.28.0
Date: 2009-10-12
Title: Simple tiling array analysis of Affymetrix ChIP-chip data
Author: Benedikt Zacher, Johannes Soeding, Pei Fen Kuan, Matthias Siebert, Achim Tresch
Maintainer: Benedikt Zacher <zacher@lmb.uni-muenchen.de>
Depends: Ringo, affy, affxparser
Imports: pspline, MASS, zlibbioc
Description: 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.
License: Artistic-2.0
biocViews:
Microarray,OneChannel,DataImport,QualityControl,Preprocessing,ChIPchip
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2016-05-04 03:16:03 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'Starr' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2  -c ahocorasick.c -o ahocorasick.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2  -c collect.c -o collect.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2  -c rm_small_peak.c -o rm_small_peak.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2  -c sort_by_genomic.c -o sort_by_genomic.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o Starr.so ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -lz -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/Starr/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'Starr'
    finding HTML links ... done
    RGlist2ExpressionSet                    html  
    backgd.sd                               html  
    bpmapToProbeAnno                        html  
    cmarrt.ma                               html  
    cmarrt.peak                             html  
    correlate                               html  
    correlationPlot                         html  
    declare.bound                           html  
    densityscatter                          html  
    expressionByFeature                     html  
    fill                                    html  
    fillNA                                  html  
    filterGenes                             html  
    getFeatures                             html  
    getIntensites                           html  
    getMeans                                html  
    getProfiles                             html  
    getProfilesByBase                       html  
    getRatio                                html  
    heatmapplot                             html  
    intersection                            html  
    kde2dplot                               html  
    list2matrix                             html  
    ma.stat                                 html  
    makeProbeAnno                           html  
    makeSplines                             html  
    mapFeatures                             html  
    match_ac                                html  
    normalize.Probes                        html  
    plot.Density                            html  
    plot.boxes                              html  
    plot.cmarrt                             html  
    plot.gcBias                             html  
    plot.image                              html  
    plot.ma                                 html  
    plot.posBias                            html  
    plot.ratioScatter                       html  
    plot.scatter                            html  
    plotProfiles                            html  
    profileplot                             html  
    rankPercentile.normalize                html  
    read.gffAnno                            html  
    readCelFile                             html  
    remap                                   html  
    rm.small.peak                           html  
    sameLength                              html  
    singleclusterplot                       html  
    sort.by.genomic                         html  
    substract                               html  
    whichIn                                 html  
    windowxy                                html  
    writeGFF                                html  
    writePosFile                            html  
    writeWIG                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Starr)
Making 'packages.html' ... done