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Starr specifications

Information


Unique identifier OMICS_00811
Name Starr
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.36.0
Stability Stable
Requirements
zlibbioc, affy, MASS, Ringo, affxparser, pspline
Maintained Yes

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Publication for Starr

Starr in publications

 (7)
PMCID: 4820846
PMID: 27025941
DOI: 10.1038/ncomms11055

[…] and averaged between replicates. smoothed signals showed a correlation of 0.75–0.87 between replicates. all analyses were carried out in r version 3.1.0. raw microarray data was analysed using the starr 1.18.1 package. nonparametric regression was done using the lowess smoothing function in r., chip-chip data for dna gyrase binding to genes in exponential phase was taken from jeong et al. […]

PMCID: 4548209
PMID: 26146939
DOI: 10.7554/eLife.06942.032

[…] (pearson correlation) also identified rb_ns12.cel as an outlier. rb_aw10.cel and rb_ns12.cel were removed from subsequent analyses. probe remapping to ncbi build 37 (mm9) was performed using the starr r package (). inputs to starr for remapping were the probe mappings for the affymetrix promoter 1.0r array and all chromosomes from the ncbi build 37 (mm9) in fasta format downloaded […]

PMCID: 4333398
PMID: 25550430
DOI: 10.1093/nar/gku1349

[…] and custom r scripting packages were used for the metagene analysis, scatterplot generation and k-means clustering. the ‘simple tiling array analysis of affymetrix chip-chip data’ (starr, ) was also used to analyse the rna pol ii chip-chip data., all the biogro samples were normalized against genomic dna (yjm789 strain) hybridized into the same custom affymetrix arrays (as […]

PMCID: 4269325
PMID: 25470042
DOI: 10.1038/nature13955

[…] specifications, and arrays were scanned using a genechip scanner 3000 7g (affymetrix). each chip-chip experiment was performed in duplicate. chip-chip data were analyzed using bioconductor package starr, for data read-in, normalizing and peak calling. quantile normalization was applied to normalize probe intensity before peak calling with default settings except that fragment length […]

PMCID: 4169242
PMID: 25232726
DOI: 10.1371/journal.pgen.1004619

[…] amplification, and chromatin and ip were separately hybridized to affymetrix drosophila tiling 2.0r arrays. the ip to chromatin ratios were computationally determined after normalisation using the starr package , and peaks identified as above, except that smoothing was over 5 probes., genes were associated to peaks if any gene feature occurred within 1 kb upstream or downstream […]


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Starr institution(s)
Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University of Munich, Munich, Germany

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