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Protocols

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

Versioning


No version available

Documentation


Publication for Starr

Starr citations

 (11)
library_books

Genome scale patterns of supercoiling in a bacterial chromosome

2016
Nat Commun
PMCID: 4820846
PMID: 27025941
DOI: 10.1038/ncomms11055

[…] Kb 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. […]

library_books

Simultaneous characterization of sense and antisense genomic processes by the double stranded hidden Markov model

2015
Nucleic Acids Res
PMCID: 4797261
PMID: 26578558
DOI: 10.1093/nar/gkv1184

[…] as these reflect the binding affinities of the pure DNA ().The ChiP–chip data we used in this work were normalized according to the protocol suggested by Zacher et al. (). This involved applying the Starr package () published in the Bioconductor project (). In order to make them comparable, data sets were finally rescaled. The 5% quantile was set to 0, and the 95% quantile was set to 1. […]

library_books

NKX2 5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets

2015
eLife
PMCID: 4548209
PMID: 26146939
DOI: 10.7554/eLife.06942.032

[…] ring (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 from the UC […]

call_split

Chromatin dependent regulation of RNA polymerases II and III activity throughout the transcription cycle

2014
Nucleic Acids Res
PMCID: 4333398
PMID: 25550430
DOI: 10.1093/nar/gku1349
call_split See protocol

[…] /tilingArray.html) 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 in ). T […]

library_books

Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle

2014
Mol Syst Biol
PMCID: 4300491
PMID: 25527639
DOI: 10.15252/msb.20145654

[…] g array (PN 520055) which tiles each strand of genomic DNA in yeast at a resolution of 8 bp. ChIP experiments were normalized using the R/Bioconductor (Ihaka & Gentleman, ; Gentleman et al, ) package Starr (Zacher et al, ) as previously described (Zacher et al, ). Expression data were normalized using the tilingArray package (Huber et al, ).The human chromatin modification dataset was downloaded f […]

call_split

TRIM37 is a new histone H2A ubiquitin ligase and breast cancer oncoprotein

2014
Nature
PMCID: 4269325
PMID: 25470042
DOI: 10.1038/nature13955
call_split See protocol

[…] ’s 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 (sonication […]

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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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