Literature DB >> 16076888

Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis.

Claire L Wilson1, Crispin J Miller.   

Abstract

UNLABELLED: Quality Control is a fundamental aspect of successful microarray data analysis. Simpleaffy is a BioConductor package that provides access to a variety of QC metrics for assessing the quality of RNA samples and of the intermediate stages of sample preparation and hybridization. Simpleaffy also offers fast implementations of popular algorithms for generating expression summaries and detection calls. AVAILABILITY: Simpleaffy can be downloaded from http://www.bioconductor.org. SUPPLEMENTARY INFORMATION: Additional information can be found on the supplementary website located at http://bioinformatics.picr.man.ac.uk.

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Year:  2005        PMID: 16076888     DOI: 10.1093/bioinformatics/bti605

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  220 in total

1.  Oxidative stress status accompanying diabetic bladder cystopathy results in the activation of protein degradation pathways.

Authors:  Nirmala D Kanika; Jinsook Chang; Yuehong Tong; Scott Tiplitsky; Juan Lin; Elizabeth Yohannes; Moses Tar; Mark Chance; George J Christ; Arnold Melman; Kelvin D Davies
Journal:  BJU Int       Date:  2010-09-21       Impact factor: 5.588

2.  Genomic analysis of between-cow variation in dermal fibroblast response to lipopolysaccharide.

Authors:  S Kandasamy; D E Kerr
Journal:  J Dairy Sci       Date:  2012-07       Impact factor: 4.034

3.  An unexpected role of semaphorin3a-neuropilin-1 signaling in lymphatic vessel maturation and valve formation.

Authors:  Giorgia Jurisic; Hélène Maby-El Hajjami; Sinem Karaman; Alexandra M Ochsenbein; Annamari Alitalo; Shoib S Siddiqui; Carlos Ochoa Pereira; Tatiana V Petrova; Michael Detmar
Journal:  Circ Res       Date:  2012-06-20       Impact factor: 17.367

4.  Candidate genes and their regulatory elements: alcohol preference and tolerance.

Authors:  Laura Saba; Sanjiv V Bhave; Nicholas Grahame; Paula Bice; Razvan Lapadat; John Belknap; Paula L Hoffman; Boris Tabakoff
Journal:  Mamm Genome       Date:  2006-06-12       Impact factor: 2.957

5.  Gene expression changes in C57BL/6J and DBA/2J mice following prenatal alcohol exposure.

Authors:  Chris Downing; Stephen Flink; Maria L Florez-McClure; Thomas E Johnson; Boris Tabakoff; Katerina J Kechris
Journal:  Alcohol Clin Exp Res       Date:  2012-04-24       Impact factor: 3.455

6.  A Set of Six Gene Expression Biomarkers Identify Rat Liver Tumorigens in Short-term Assays.

Authors:  J Christopher Corton; Thomas Hill; Jeffrey J Sutherland; James L Stevens; John Rooney
Journal:  Toxicol Sci       Date:  2020-09-01       Impact factor: 4.849

7.  Nicotinamide mononucleotide requires SIRT3 to improve cardiac function and bioenergetics in a Friedreich's ataxia cardiomyopathy model.

Authors:  Angelical S Martin; Dennis M Abraham; Kathleen A Hershberger; Dhaval P Bhatt; Lan Mao; Huaxia Cui; Juan Liu; Xiaojing Liu; Michael J Muehlbauer; Paul A Grimsrud; Jason W Locasale; R Mark Payne; Matthew D Hirschey
Journal:  JCI Insight       Date:  2017-07-20

8.  Transcriptional atlas of cardiogenesis maps congenital heart disease interactome.

Authors:  Xing Li; Almudena Martinez-Fernandez; Katherine A Hartjes; Jean-Pierre A Kocher; Timothy M Olson; Andre Terzic; Timothy J Nelson
Journal:  Physiol Genomics       Date:  2014-05-06       Impact factor: 3.107

9.  Thermodynamic scaling behavior in genechips.

Authors:  Alessandro Ferrantini; Joke Allemeersch; Paul Van Hummelen; Enrico Carlon
Journal:  BMC Bioinformatics       Date:  2009-01-06       Impact factor: 3.169

10.  Time course differential gene expression in response to porcine circovirus type 2 subclinical infection.

Authors:  Anna Tomás; Lana T Fernandes; Armand Sánchez; Joaquim Segalés
Journal:  Vet Res       Date:  2009-10-14       Impact factor: 3.683

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