Literature DB >> 25633503

Orchestrating high-throughput genomic analysis with Bioconductor.

Wolfgang Huber1, Vincent J Carey2, Robert Gentleman3, Simon Anders1, Marc Carlson4, Benilton S Carvalho5, Hector Corrada Bravo6, Sean Davis7, Laurent Gatto8, Thomas Girke9, Raphael Gottardo10, Florian Hahne11, Kasper D Hansen12, Rafael A Irizarry13, Michael Lawrence3, Michael I Love13, James MacDonald14, Valerie Obenchain4, Andrzej K Oleś1, Hervé Pagès4, Alejandro Reyes1, Paul Shannon4, Gordon K Smyth15, Dan Tenenbaum4, Levi Waldron16, Martin Morgan4.   

Abstract

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.

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Year:  2015        PMID： 25633503      PMCID： PMC4509590          DOI： 10.1038/nmeth.3252

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  21 in total

1.  Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

2.  Reproducible research: a bioinformatics case study.

Authors:  Robert Gentleman
Journal:  Stat Appl Genet Mol Biol       Date:  2005-01-11

3.  Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping.

Authors:  Christina Laufer; Bernd Fischer; Maximilian Billmann; Wolfgang Huber; Michael Boutros
Journal:  Nat Methods       Date:  2013-04-07       Impact factor: 28.547

4.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

5.  Bioconductor: open software development for computational biology and bioinformatics.

Authors:  Robert C Gentleman; Vincent J Carey; Douglas M Bates; Ben Bolstad; Marcel Dettling; Sandrine Dudoit; Byron Ellis; Laurent Gautier; Yongchao Ge; Jeff Gentry; Kurt Hornik; Torsten Hothorn; Wolfgang Huber; Stefano Iacus; Rafael Irizarry; Friedrich Leisch; Cheng Li; Martin Maechler; Anthony J Rossini; Gunther Sawitzki; Colin Smith; Gordon Smyth; Luke Tierney; Jean Y H Yang; Jianhua Zhang
Journal:  Genome Biol       Date:  2004-09-15       Impact factor: 13.583

6.  Software for computing and annotating genomic ranges.

Authors:  Michael Lawrence; Wolfgang Huber; Hervé Pagès; Patrick Aboyoun; Marc Carlson; Robert Gentleman; Martin T Morgan; Vincent J Carey
Journal:  PLoS Comput Biol       Date:  2013-08-08       Impact factor: 4.475

7.  Detecting differential usage of exons from RNA-seq data.

Authors:  Simon Anders; Alejandro Reyes; Wolfgang Huber
Journal:  Genome Res       Date:  2012-06-21       Impact factor: 9.043

8.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Authors:  Jeremy Goecks; Anton Nekrutenko; James Taylor
Journal:  Genome Biol       Date:  2010-08-25       Impact factor: 13.583

9.  Differential expression analysis for sequence count data.

Authors:  Simon Anders; Wolfgang Huber
Journal:  Genome Biol       Date:  2010-10-27       Impact factor: 13.583

10.  An integrated encyclopedia of DNA elements in the human genome.

Authors: 
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962
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  1214 in total

1.  The genetic fingerprint of susceptibility for transplant-associated thrombotic microangiopathy.

Authors:  Sonata Jodele; Kejian Zhang; Fanggeng Zou; Benjamin Laskin; Christopher E Dandoy; Kasiani C Myers; Adam Lane; Jaroslav Meller; Mario Medvedovic; Jenny Chen; Stella M Davies
Journal:  Blood       Date:  2015-11-24       Impact factor: 22.113

2.  Alcohol Consumption Modulates Host Defense in Rhesus Macaques by Altering Gene Expression in Circulating Leukocytes.

Authors:  Tasha Barr; Thomas Girke; Suhas Sureshchandra; Christina Nguyen; Kathleen Grant; Ilhem Messaoudi
Journal:  J Immunol       Date:  2015-11-30       Impact factor: 5.422

3.  Next-generation sequencing of 100 candidate genes in young victims of suspected sudden cardiac death with structural abnormalities of the heart.

Authors:  C L Hertz; S L Christiansen; L Ferrero-Miliani; M Dahl; P E Weeke; G L Ottesen; R Frank-Hansen; H Bundgaard; N Morling
Journal:  Int J Legal Med       Date:  2015-09-17       Impact factor: 2.686

4.  The natverse, a versatile toolbox for combining and analysing neuroanatomical data.

Authors:  Alexander Shakeel Bates; James D Manton; Sridhar R Jagannathan; Marta Costa; Philipp Schlegel; Torsten Rohlfing; Gregory Sxe Jefferis
Journal:  Elife       Date:  2020-04-14       Impact factor: 8.140

5.  Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability.

Authors:  Lindsay F Rizzardi; Peter F Hickey; Varenka Rodriguez DiBlasi; Rakel Tryggvadóttir; Colin M Callahan; Adrian Idrizi; Kasper D Hansen; Andrew P Feinberg
Journal:  Nat Neurosci       Date:  2019-01-14       Impact factor: 24.884

6.  HSP90 inhibitor geldanamycin reverts IL-13- and IL-17-induced airway goblet cell metaplasia.

Authors:  Alejandro A Pezzulo; Rosarie A Tudas; Carley G Stewart; Luis G Vargas Buonfiglio; Brian D Lindsay; Peter J Taft; Nicholas D Gansemer; Joseph Zabner
Journal:  J Clin Invest       Date:  2019-01-14       Impact factor: 14.808

7.  Revealing Dynamic Protein Acetylation across Subcellular Compartments.

Authors:  Josue Baeza; Alexis J Lawton; Jing Fan; Michael J Smallegan; Ian Lienert; Tejas Gandhi; Oliver M Bernhardt; Lukas Reiter; John M Denu
Journal:  J Proteome Res       Date:  2020-04-27       Impact factor: 4.466

8.  A transcription factor collective defines the HSN serotonergic neuron regulatory landscape.

Authors:  Carla Lloret-Fernández; Miren Maicas; Carlos Mora-Martínez; Alejandro Artacho; Ángela Jimeno-Martín; Laura Chirivella; Peter Weinberg; Nuria Flames
Journal:  Elife       Date:  2018-03-22       Impact factor: 8.140

9.  Genetic susceptibility to toxicologic lung responses among inbred mouse strains following exposure to carbon nanotubes and profiling of underlying gene networks.

Authors:  Evan A Frank; Vinicius S Carreira; Kumar Shanmukhappa; Mario Medvedovic; Daniel R Prows; Jagjit S Yadav
Journal:  Toxicol Appl Pharmacol       Date:  2017-04-19       Impact factor: 4.219

10.  Nonparametric expression analysis using inferential replicate counts.

Authors:  Anqi Zhu; Avi Srivastava; Joseph G Ibrahim; Rob Patro; Michael I Love
Journal:  Nucleic Acids Res       Date:  2019-10-10       Impact factor: 16.971
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