Open AccessPosted Content
Bioconductor: Open Software Development for Computational Biology and Bioinformatics
Kurt Hornik,Robert Gentleman,Vincent J. Carey,Douglas M. Bates,Ben Bolstad,Marcel Dettling,Sandrine Dudoit,Byron Ellis,Laurent Gautier,Yongchao Ge,Jeff Gentry,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 Y.H. Yang,Jean Y.H. Yang,Jianhua Zhang +25 more
TL;DR: The Bioconductor project as discussed by the authors is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics, which aims to foster collaborative development and widespread use of innovative software, reduce barriers to entry into interdisciplinary scientific research, and promote the achievement of remote reproducibility of research results.
read more
Abstract: The Bioconductor project is an initiative for the collaborative creation of the extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methodes, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features
TL;DR: FeatureCounts as discussed by the authors is a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments, which implements highly efficient chromosome hashing and feature blocking techniques.
22.7K
Waste not, want not: why rarefying microbiome data is inadmissible.
Paul J. McMurdie,Susan Holmes +1 more
TL;DR: It is advocated that investigators avoid rarefying altogether and supported statistical theory is provided that simultaneously accounts for library size differences and biological variability using an appropriate mixture model.
MAST: A flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA-seq data
Greg Finak,Andrew McDavid,Masanao Yajima,Jingyuan Deng,Vivian H. Gersuk,Alex K. Shalek,Chloe K. Slichter,Hannah W. Miller,M. Juliana McElrath,Martin Prlic,Peter S. Linsley,Raphael Gottardo +11 more
TL;DR: A new methodology to analyze single-cell transcriptomic data is presented that models this bimodality within a coherent generalized linear modeling framework, and the cellular detection rate, the fraction of genes turned on in a cell, is introduced.
Mesenchymal Stem Cell-Derived Microvesicles Protect Against Acute Tubular Injury
Stefania Bruno,Cristina Grange,Maria Chiara Deregibus,Raffaele A. Calogero,Silvia Saviozzi,Federica Collino,Laura Morando,Alessandro Busca,Michele Falda,Benedetta Bussolati,Ciro Tetta,Giovanni Camussi +11 more
TL;DR: It is found that microvesicles derived from human bone marrow MSCs stimulated proliferation in vitro and conferred resistance of tubular epithelial cells to apoptosis, suggesting RNA-dependent biologic effects.
References
The Bioperl Toolkit: Perl Modules for the Life Sciences
Jason E. Stajich,David Block,David Block,Kris Boulez,Steven E. Brenner,Stephen A. Chervitz,Chris Dagdigian,Georg Fuellen,James G. R. Gilbert,Ian F Korf,Hilmar Lapp,Heikki Lehväslaiho,Chad Matsalla,Christopher J. Mungall,Brian I. Osborne,Matthew Pocock,Peter Schattner,Martin Senger,Lincoln Stein,Elia Stupka,Mark Wilkinson,Ewan Birney +21 more
TL;DR: The overall architecture of the Bioperl toolkit is described, the problem domains that it addresses, and specific examples of how the toolkit can be used to solve common life-sciences problems are given.
•Book
The Cathedral and the Bazaar
Eric S. Raymond,Tim O'Reilly +1 more
- 01 Jan 1999
TL;DR: Open source software brings to the computer software industry even greater freedom than the hardware manufacturers and consumers have enjoyed as mentioned in this paper, instead of enabling the vendors to control their customers through restricting access to the code behind the technologies.
874
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,Xiaochun Li,Robert Gentleman,Robert Gentleman,Antonella Vitale,Antonella Vitale,Marco Vignetti,Marco Vignetti,Franco Mandelli,Franco Mandelli,Jerome Ritz,Robin Foà,Robin Foà +13 more
TL;DR: It is demonstrated that gene expression profiling can identify a limited number of genes that are predictive of response to induction therapy and remission duration in adult patients with T-ALL.
424
Creating a bioinformatics nation
TL;DR: A web-services model will allow biological data to be fully exploited and is likely to be adopted in the coming years.
369
Statistical Analyses and Reproducible Research
TL;DR: This article describes a software framework for both authoring and distributing integrated, dynamic documents that contain text, code, data, and any auxiliary content needed to recreate the computations in data analyses, methodological descriptions, simulations, and so on.