Bioconductor: open software development for computational biology and bioinformatics

Keywords

Bioconductor, Software, Biology, Data science, Bioinformatics

References

• Expression Array Annotation Using the BioMediator Biological Data Integration System and the BioConductor Analytic PlatformHao Mei, Peter Tarczy‐Hornoch, Peter Mork — 2003
• Literate Statistical PracticeAnthony Rossini, Friedrich Leisch — 2003
• A pocket referenceEric Shepherd — 1994
• Simple object access protocol (SOAP) 1.1Donald F. Box — 2000
• The Boost Graph Library - User Guide and Reference ManualJeremy G. Siek, Lie‐Quan Lee, Andrew Lumsdaine — 2001
• Review of "The boost graph library: user guide and reference manual by Jeremy G. Siek, Lie-Quan Lee, and Andrew Lumsdaine." Addison-Wesley 2002.Jim Law — 2003
• Programming With Data: A Guide to the S LanguageDouglas M. Bates — 1998
• Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection.Cheng Li, Wing Hung Wong — 2001
• The cathedral and the bazaarEric S. Raymond — 1998
• The Linux edgeLinus Torvalds — 1999
• Creating a bioinformatics nationLincoln Stein — 2002
• Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival.Sabina Chiaretti, Xiaochun Li, Robert Gentleman — 2004
• Management and Virtual Decentralised Networks: The Linux ProjectGeorge Dafermos — 2001
• Common Lisp the LanguageGuy L. Steele — 1984
• An extensible application for assembling annotation for genomic dataJianhua Zhang, Vincent J. Carey, Robert Gentleman — 2003
• Making scientific computations reproducibleMatthias Schwab, N. Karrenbach, Jon F. Claerbout — 2000
• The Bioperl toolkit: Perl modules for the life sciences.Jason Stajich, David E. Block, Kris Boulez — 2002
• Monte Carlo and quasi-Monte Carlo methodsRussel E. Caflisch — 1998
• Simple Object Access Protocol (SOAP)Regina Dunlea — 2005
• CVS Pocket ReferenceGregor N. Purdy — 2000

Cited by

• Unraveling the Role of Hemeoxygenase-1/Carbon Monoxide in Pulmonary and Cardiovascular Diseases.Anuli C. Anyanwu — 2013
• Interpretation of gene expression microarray experimentsAristotelis Chatziioannou, Panagiotis Moulos — 2007
• Variants of the Consecutive Ones Property: Algorithms, Computational Complexity and Applications to GenomicsAshok Rajaraman — 2015
• ACGT: Advancing Clinico-genomic trials on cancer - Four years of experienceLuis Martín, Alberto Anguita, Norbert Graf — 2011
• Role of Inflammation in Diet-Induced Obesity: A DissertationSophia Kogan — 2013
• Developer-Friendly and Computationally Efficient Predictive Modeling without Information Leakage: The emil Package for RChristofer Bäcklin, Mats G. Gustafsson — 2018
• Designing, performing, and interpreting a microarray-based gene expression study.Giovanni Coppola — 2011
• Modeling, simulation and analysis of methylation profiles from reduced representation bisulfite sequencing experimentsMichelle Lacey, Carl Baribault, Melanie Ehrlich — 2013
• Systems Analysis of High–Throughput DataRosemary Braun — 2014
• Analysis of phosphoproteomics data.Christoph Schaab — 2011
• Machine Learning Based Analysis of DNA Methylation Patterns in Pediatric Acute LeukemiaChristofer Bäcklin — 2015
• CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genomeCarlos Lomas, Isabel Gracida — 2005
• Gene expression profiling reveals a signaling role of glutathione in redox regulation.Raymond T Pollard, I. Waddington, Kevin D. Browne — 2005
• Down-regulation of stem cell genes, including those in a 200-kb gene cluster at 12p13.31, is associated with in vivo differentiation of human male germ cell tumors.В. Я. Белокреницкий — 2006
• Zfp206 regulates ES cell gene expression and differentiationPeter van Zilfhout — 2006
• Thermoregulatory and metabolic defects in Huntington's disease transgenic mice implicate PGC-1alpha in Huntington's disease neurodegeneration.S. N. Yurchenko, P. R. Bunker, W.P. Kraemer — 2006
• Differential Gene Expression in Cultured Osteoblasts and Bone Marrow Stromal Cells From Patients With Paget's Disease of BoneAlberto Casado Cerviño — 2006
• Hematopoietic progenitor cells (HPC) from mobilized peripheral blood display enhanced migration and marrow homing compared to steady-state bone marrow HPC.Maggi Sietsma-Smith — 2007
• Genome‐wide expression profiling during protection from colitis by regulatory T cellsY. M. El-Sayed — 2008
• RReportGenerator: automatic reports from routine statistical analysis using RWolfgang Raffelsberger, Yannick Krause, Luc Moulinier — 2008

Related papers

• CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAsBart P.P. van Houte, Thomas W. Binsl, Hannes Hettling — 2010
• Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductorMichał Okoniewski, Crispin Miller — 2008
• easyRNASeq: a bioconductor package for processing RNA-Seq dataNicolas Delhomme, Ismaël Padioleau, Eileen E. M. Furlong — 2012
• girafe – an R/Bioconductor package for functional exploration of aligned next-generation sequencing readsJoern Toedling, Constance Ciaudo, Olivier Voinnet — 2010
• CAGEfightR: analysis of 5′-end data using R/BioconductorMalte Thodberg, Axel Thieffry, Kristoffer Vitting‐Seerup — 2019
• rTANDEM, an R/Bioconductor package for MS/MS protein identificationFrédéric Fournier, Charles Joly Beauparlant, René Paradis — 2014
• A framework for oligonucleotide microarray preprocessingBenilton S. Carvalho, Rafael A. Irizarry — 2010
• Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequencesJiří Hon, Tomáš Martínek, Kamil Rajdl — 2013
• gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profilesFrancesco Napolitano, Diego Carrella, Xin Gao — 2019
• BioConductor: Microarray versus Next-Generation Sequencing toolsetsSander Bollen — 2014