Orchestrating high-throughput genomic analysis with Bioconductor
Wolfgang Huber,Vincent J. Carey,Robert Gentleman,Simon Anders,Marc R. J. Carlson,Benilton S. Carvalho,Héctor Corrada Bravo,Sean Davis,Laurent Gatto,Thomas Girke,Raphael Gottardo,Florian Hahne,Kasper D. Hansen,Rafael A. Irizarry,Michael S. Lawrence,Michael I. Love,James W. MacDonald,Valerie Obenchain,Andrzej K. Oleś,Hervé Pagès,Alejandro Reyes,Paul Shannon,Gordon K. Smyth,Dan Tenenbaum,Levi Waldron,Martin Morgan +25 more
Reads0
Chats0
TLDR
An overview of Bioconductor, an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology, which comprises 934 interoperable packages contributed by a large, diverse community of scientists.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.read more
Citations
More filters
Journal ArticleDOI
Mitochondrial autophagy and cell survival is regulated by the circadian Clock gene in cardiac myocytes during ischemic stress.
Inna Rabinovich-Nikitin,Mina Rasouli,Cristine J. Reitz,Illana Posen,Victoria Margulets,Rimpy Dhingra,Tarak N. Khatua,James A. Thliveris,Tami A. Martino,Lorrie A. Kirshenbaum +9 more
TL;DR: In this paper, a putative circadian clock-mitochondrial interactome was identified that gates an adaptive survival response during myocardial ischemia, and it was shown by transcriptome and gene ontology mapping in a CLOCK Δ19/Δ19 mouse that Clock transcriptionally coordinates the efficient removal of damaged mitochondria during acute hypoxia by directly controlling transcription of genes required for mitochondrial fission, fusion and macroautophagy/autophagia.
Journal ArticleDOI
Methylomic Analysis of Ovarian Cancers Identifies Tumor-Specific Alterations Readily Detectable in Early Precursor Lesions.
Thomas R. Pisanic,Leslie Cope,Shiou Fu Lin,Ting Tai Yen,Pornpat Athamanolap,Ryoichi Asaka,Kentaro Nakayama,Amanda Nickles Fader,Tza-Huei Wang,Ie Ming Shih,Tian Li Wang +10 more
TL;DR: A panel of methylation biomarkers can be used to accurately identify HGSOC, even at precursor stages of the disease.
Posted ContentDOI
Evolutionary stability of topologically associating domains is associated with conserved gene regulation
TL;DR: The results indicate that TADs are conserved building blocks of genomes with regulatory functions that are often reshuffled as a whole instead of being disrupted by rearrangements.
Journal ArticleDOI
A data-driven approach to estimating the number of clusters in hierarchical clustering.
TL;DR: In this article, the authors proposed two new methods (mode and maximum difference) for estimating the number of clusters in a hierarchical clustering framework to create a fully automated process with no human intervention.
Journal ArticleDOI
Time-Dependent Molecular Responses Differ between Gastric Bypass and Dieting but Are Conserved Across Species
Danny Ben-Zvi,Danny Ben-Zvi,Danny Ben-Zvi,Luca Meoli,Wasif M. Abidi,Eirini Nestoridi,Courtney Panciotti,Erick Castillo,Palmenia Pizarro,Eleanor Shirley,William Gourash,Christopher C. Thompson,Rodrigo Muñoz,Clary B. Clish,Ron C. Anafi,Anita P. Courcoulas,Nicholas Stylopoulos,Nicholas Stylopoulos +17 more
TL;DR: It is shown that, although dieting and RYGB can bring about the same degree of weight loss, post-RYGB physiology is very different.
References
More filters
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
An integrated encyclopedia of DNA elements in the human genome
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal ArticleDOI
Differential expression analysis for sequence count data.
Simon Anders,Wolfgang Huber +1 more
TL;DR: A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.
Journal ArticleDOI
Bioconductor: open software development for computational biology and bioinformatics
Robert Gentleman,Vincent J. Carey,Douglas M. Bates,Benjamin M. Bolstad,Marcel Dettling,Sandrine Dudoit,Byron Ellis,Laurent Gautier,Yongchao Ge,Jeff Gentry,Kurt Hornik,Torsten Hothorn,Wolfgang Huber,Stefano Maria Iacus,Rafael A. Irizarry,Friedrich Leisch,Cheng Li,Martin Maechler,A. J. Rossini,Günther Sawitzki,Colin A. Smith,Gordon K. Smyth,Luke Tierney,Jean Yang,Jianhua Zhang +24 more
TL;DR: Details of the aims and methods of Bioconductor, the collaborative creation of extensible software for computational biology and bioinformatics, and current challenges are described.
Journal ArticleDOI
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Alvis Brazma,Pascal Hingamp,John Quackenbush,Gavin Sherlock,Paul T. Spellman,Chris Stoeckert,John Aach,Wilhelm Ansorge,Catherine A. Ball,Helen C. Causton,Terry Gaasterland,Patrick Glenisson,Frank C. P. Holstege,Irene F. Kim,Victor Markowitz,John C. Matese,Helen Parkinson,Alan J. Robinson,Ugis Sarkans,Steffen Schulze-Kremer,Jason E. Stewart,Ronald C. Taylor,Jaak Vilo,Martin Vingron +23 more
TL;DR: The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools.
Related Papers (5)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more