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Bioconductor: Open Software Development for Computational Biology and Bioinformatics Robert C
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Collection Of Biostatistics Research Archive Bioconductor Project Bioconductor Project Working Papers Year 2004 Paper 1 Bioconductor: Open software development for computational biology and bioinformatics Robert C. Gentleman, Department of Biostatistical Sciences, Dana Farber Can- cer Institute Vincent J. Carey, Channing Laboratory, Brigham and Women’s Hospital Douglas J. Bates, Department of Statistics, University of Wisconsin, Madison Benjamin M. Bolstad, Division of Biostatistics, University of California, Berkeley Marcel Dettling, Seminar for Statistics, ETH, Zurich, CH Sandrine Dudoit, Division of Biostatistics, University of California, Berkeley Byron Ellis, Department of Statistics, Harvard University Laurent Gautier, Center for Biological Sequence Analysis, Technical University of Denmark, DK Yongchao Ge, Department of Biomathematical Sciences, Mount Sinai School of Medicine Jeff Gentry, Department of Biostatistical Sciences, Dana Farber Cancer Institute Kurt Hornik, Computational Statistics Group, Department of Statistics and Math- ematics, Wirtschaftsuniversitat¨ Wien, AT Torsten Hothorn, Institut fuer Medizininformatik, Biometrie und Epidemiologie, Friedrich-Alexander-Universitat Erlangen-Nurnberg, DE Wolfgang Huber, Department for Molecular Genome Analysis (B050), German Cancer Research Center, Heidelberg, DE Stefano Iacus, Department of Economics, University of Milan, IT Rafael Irizarry, Department of Biostatistics, Johns Hopkins University Friedrich Leisch, Institut fur¨ Statistik und Wahrscheinlichkeitstheorie, Technische Universitat¨ Wien, AT Cheng Li, Department of Biostatistical Sciences, Dana Farber Cancer Institute Martin Maechler, Seminar for Statistics, ETH, Zurich, CH Anthony J. Rossini, Department of Medical Education and Biomedical Informat- ics, University of Washington Guenther Sawitzki, Statistisches Labor, Institut fuer Angewandte Mathematik, DE Colin Smith, Department of Molecular Biology, The Scripps Research Institute, San Diego Gordon K. -
Backbox Penetration Testing Never Looked So Lovely
DISTROHOPPER DISTROHOPPER Our pick of the latest releases will whet your appetite for new Linux distributions. Picaros Diego Linux for children. here are a few distributions aimed at children: Doudou springs to mind, Tand there’s also Sugar on a Stick. Both of these are based on the idea that you need to protect children from the complexities of the computer (and protect the computer from the children). Picaros Diego is different. There’s nothing stripped- down or shielded from view. Instead, it’s a normal Linux distro with a brighter, more kid-friendly interface. The desktop wallpaper perhaps best We were too busy playing Secret Mario on Picaros Diego to write a witty or interesting caption. exemplifies this. On one hand, it’s a colourful cartoon image designed to interest young file manager. In the programming category, little young for a system like this, but the it children. Some of the images on the we were slightly disappointed to discover it may well work for children on the upper end landscape are icons for games, and this only had Gambas (a Visual Basic-like of that age range. should encourage children to investigate the language), and not more popular teaching Overall, we like the philosophy of wrapping system rather than just relying on menus. languages like Scratch or a Python IDE. Linux is a child-friendly package, but not On the other hand, it still displays technical However, it’s based on Debian, so you do dumbing it down. Picaros Diego won’t work details such as the CPU usage and the RAM have the full range of software available for every child, but if you have a budding and Swap availability. -
Statistical Computing with Pathway Tools Using Rcyc
Statistical Computing with Pathway Tools using RCyc Statistical Computing with Pathway Tools using RCyc Tomer Altman [email protected] Biomedical Informatics, Stanford University Statistical Computing with Pathway Tools using RCyc R & BioConductor S: software community over 30 years of statistical computing, data mining, machine learning, and data visualization knowledge R: open-source S with a lazy Scheme interpreter at its heart (including closures, symbols, and even macros!) RCyc: an R package to allow the interaction between Pathway / Genome Databases and the wealth of biostatistics software in the R community Statistical Computing with Pathway Tools using RCyc BioConductor Figure: BioConductor: Thousands of peer-reviewed biostatistics packages. Statistical Computing with Pathway Tools using RCyc Software`R'-chitecture C code extension to R to allow Unix socket access Common Lisp code to hack in XML-based communication Make the life of *Cyc API developers easier. Currently supports exchange of numbers, strings, and lists R code and documentation Provides utilities for starting PTools and marshaling data types Assumes user is familiar with the PTools API: http://bioinformatics.ai.sri.com/ptools/api/ All wrapped up in R package Easily installs via standard command-line R interface Statistical Computing with Pathway Tools using RCyc Simple Example callPToolsFn("so",list("'meta")) callPToolsFn("get-slot-value",list("'proton", "'common-name")) callPToolsFn("get-class-all-instances",list("'|Reactions|")) Statistical Computing with Pathway Tools using RCyc Availability http://github.com/taltman/RCyc Linked from PTools website Statistical Computing with Pathway Tools using RCyc Next Steps Dynamic instantiation of API functions in R Coming next release (coordination with BRG) Make development of *Cyc APIs easier, less boilerplate code Frame to Object import/export Provide \RCelot" functionality to slurp Ocelot frames directly into R S4 reference objects for direct data access Support for more exotic data types Symbols, hash tables, arrays, structures, etc. -
Navigating the R Package Universe by Julia Silge, John C
CONTRIBUTED RESEARCH ARTICLES 558 Navigating the R Package Universe by Julia Silge, John C. Nash, and Spencer Graves Abstract Today, the enormous number of contributed packages available to R users outstrips any given user’s ability to understand how these packages work, their relative merits, or how they are related to each other. We organized a plenary session at useR!2017 in Brussels for the R community to think through these issues and ways forward. This session considered three key points of discussion. Users can navigate the universe of R packages with (1) capabilities for directly searching for R packages, (2) guidance for which packages to use, e.g., from CRAN Task Views and other sources, and (3) access to common interfaces for alternative approaches to essentially the same problem. Introduction As of our writing, there are over 13,000 packages on CRAN. R users must approach this abundance of packages with effective strategies to find what they need and choose which packages to invest time in learning how to use. At useR!2017 in Brussels, we organized a plenary session on this issue, with three themes: search, guidance, and unification. Here, we summarize these important themes, the discussion in our community both at useR!2017 and in the intervening months, and where we can go from here. Users need options to search R packages, perhaps the content of DESCRIPTION files, documenta- tion files, or other components of R packages. One author (SG) has worked on the issue of searching for R functions from within R itself in the sos package (Graves et al., 2017). -
Other Departments and Institutes Courses 1
Other Departments and Institutes Courses 1 Other Departments and Institutes Courses About Course Numbers: 02-250 Introduction to Computational Biology Each Carnegie Mellon course number begins with a two-digit prefix that Spring: 12 units designates the department offering the course (i.e., 76-xxx courses are This class provides a general introduction to computational tools for biology. offered by the Department of English). Although each department maintains The course is divided into two halves. The first half covers computational its own course numbering practices, typically, the first digit after the prefix molecular biology and genomics. It examines important sources of biological indicates the class level: xx-1xx courses are freshmen-level, xx-2xx courses data, how they are archived and made available to researchers, and what are sophomore level, etc. Depending on the department, xx-6xx courses computational tools are available to use them effectively in research. may be either undergraduate senior-level or graduate-level, and xx-7xx In the process, it covers basic concepts in statistics, mathematics, and courses and higher are graduate-level. Consult the Schedule of Classes computer science needed to effectively use these resources and understand (https://enr-apps.as.cmu.edu/open/SOC/SOCServlet/) each semester for their results. Specific topics covered include sequence data, searching course offerings and for any necessary pre-requisites or co-requisites. and alignment, structural data, genome sequencing, genome analysis, genetic variation, gene and protein expression, and biological networks and pathways. The second half covers computational cell biology, including biological modeling and image analysis. It includes homework requiring Computational Biology Courses modification of scripts to perform computational analyses. -
Bioconductor: Open Software Development for Computational Biology and Bioinformatics Robert C
Bioconductor Project Bioconductor Project Working Papers Year 2004 Paper 1 Bioconductor: Open software development for computational biology and bioinformatics Robert C. Gentleman, Department of Biostatistical Sciences, Dana Farber Can- cer Institute Vincent J. Carey, Channing Laboratory, Brigham and Women’s Hospital Douglas J. Bates, Department of Statistics, University of Wisconsin, Madison Benjamin M. Bolstad, Division of Biostatistics, University of California, Berkeley Marcel Dettling, Seminar for Statistics, ETH, Zurich, CH Sandrine Dudoit, Division of Biostatistics, University of California, Berkeley Byron Ellis, Department of Statistics, Harvard University Laurent Gautier, Center for Biological Sequence Analysis, Technical University of Denmark, DK Yongchao Ge, Department of Biomathematical Sciences, Mount Sinai School of Medicine Jeff Gentry, Department of Biostatistical Sciences, Dana Farber Cancer Institute Kurt Hornik, Computational Statistics Group, Department of Statistics and Math- ematics, Wirtschaftsuniversitat¨ Wien, AT Torsten Hothorn, Institut fuer Medizininformatik, Biometrie und Epidemiologie, Friedrich-Alexander-Universitat Erlangen-Nurnberg, DE Wolfgang Huber, Department for Molecular Genome Analysis (B050), German Cancer Research Center, Heidelberg, DE Stefano Iacus, Department of Economics, University of Milan, IT Rafael Irizarry, Department of Biostatistics, Johns Hopkins University Friedrich Leisch, Institut fur¨ Statistik und Wahrscheinlichkeitstheorie, Technische Universitat¨ Wien, AT Cheng Li, Department -
Linux Virtual COM User's Manual
LES301A-KIT LES301AE-KIT LES302A-KIT LES302AE-KIT 1- and 2-Port 10/100 Device Servers, RS-232/422/485, DB9 M Linux Virtual COM User’s Manual ® BLAC K BOX Customer Order toll-free in the U.S.: Call 877-877-BBOX (outside U.S. call 724-746-5500) Support FREE technical support 24 hours a day, 7 days a week: Call 724-746-5500 or fax 724-746-0746 Mailing address: Black Box Corporation, 1000 Park Drive, Lawrence, PA 15055-1018 Information Web site: www.blackbox.com • E-mail: [email protected] Linux Virtual COM user manual Trademarks Used in this Manual Trademarks Used in this Manual Black Box and the Double Diamond logo are registered trademarks of BB Technologies, Inc. Ubuntu is a registered trademark of Canonical Ltd. Linux is a registered trademark of Linus Torvalds. SUSE is a registered trademark of Novell, Inc. Red Hat and Fedora are registered trademarks of Red Hat, Inc. Debian is a registered trademark of Software in the Public Interest, Inc. Any other trademarks mentioned in this manual are acknowleged to be the property of the trademark owners. We‘re here to help! If you have any questions about your application or our products, contact Black Box Tech Support at 724-746-5500 or go to blackbox.com and click on “Talk to Black Box.” You’ll be live with one of our technical experts in less than 30 seconds. Page 2 724-746-5500 | blackbox.com Linux Virtual COM user manual 724-746-5500 | blackbox.com Guides Contained in this Document IMPORTANT ANNOUNCEMENT: The information contained in this document is the property of Black Box Corporation and is supplied for the sole purpose of the operation and maintenance of products of Black Box Corporation. -
Decode™ Bioinformatic Analysis
PROTOCOL Decode™ Bioinformatic Analysis An introductory guide for the use of high-throughput sequencing to determine primary hits from an shRNA pooled screen. Table of contents 1. Legal disclaimers 1. Legal disclaimers 1 SOFTWARE LICENSE TERMS. With respect to any software products 2. Summary 2 incorporated in or forming a part of the software provided or described 3. Intended audience 2 hereunder (“Software”), Horizon Discovery (“Seller”) and you, the purchaser, 4. Software requirements 2 licensee and/or end-user of the software (“Buyer”) intend and agree that 5. FASTQ files from high-throughput sequencing 2 such software products are being licensed and not sold, and that the words 6. Align the FASTQ files to reference shRNA FASTA files 3 “purchase”, “sell” or similar or derivative words are understood and agreed to A. Create a Bowtie index 3 mean “license”, and that the word “Buyer” or similar or derivative words are B. Align using Bowtie 3 understood and agreed to mean “licensee”. Notwithstanding anything to the C. Batch process 4 contrary contained herein, Seller or its licensor, as the case may be, retains all D. Alignment summaries 4 rights and interest in software products provided hereunder. 7. Differential expression analysis 5 A. Convert Bowtie files into DESeq input 5 Seller hereby grants to Buyer a royalty-free, non-exclusive, nontransferable B. Run DESeq on .rtable files 7 license, without power to sublicense, to use software provided hereunder 8. Conclusions 9 solely for Buyer’s own internal business purposes and to use the related documentation solely for Buyer’s own internal business purposes. -
R / Bioconductor for High-Throughput Sequence Analysis
R / Bioconductor for High-Throughput Sequence Analysis Nicolas Delhomme1 21 October - 26 October, 2013 [email protected] Contents 1 Day2 of the workshop2 1.1 Introduction............................................2 1.2 Main Bioconductor packages of interest for the day......................2 1.3 A word on High-throughput sequence analysis.........................2 1.4 A word on Integrated Development Environment (IDE)...................2 1.5 Today's schedule.........................................2 2 Prelude 4 2.1 Purpose..............................................4 2.2 Creating GAlignment objects from BAM files.........................4 2.3 Processing the files in parallel..................................4 2.4 Processing the files one chunk at a time............................5 2.5 Pros and cons of the current solution..............................6 2.5.1 Pros............................................6 2.5.2 Cons............................................6 3 Sequences and Short Reads7 3.1 Alignments and Bioconductor packages............................7 3.1.1 The pasilla data set...................................7 3.1.2 Alignments and the ShortRead package........................8 3.1.3 Alignments and the Rsamtools package........................9 3.1.4 Alignments and other Bioconductor packages..................... 13 3.1.5 Resources......................................... 17 4 Interlude 18 5 Estimating Expression over Genes and Exons 20 5.1 Counting reads over known genes and exons.......................... 20 5.1.1 -
Introduction to Ggplot2
Introduction to ggplot2 Dawn Koffman Office of Population Research Princeton University January 2014 1 Part 1: Concepts and Terminology 2 R Package: ggplot2 Used to produce statistical graphics, author = Hadley Wickham "attempt to take the good things about base and lattice graphics and improve on them with a strong, underlying model " based on The Grammar of Graphics by Leland Wilkinson, 2005 "... describes the meaning of what we do when we construct statistical graphics ... More than a taxonomy ... Computational system based on the underlying mathematics of representing statistical functions of data." - does not limit developer to a set of pre-specified graphics adds some concepts to grammar which allow it to work well with R 3 qplot() ggplot2 provides two ways to produce plot objects: qplot() # quick plot – not covered in this workshop uses some concepts of The Grammar of Graphics, but doesn’t provide full capability and designed to be very similar to plot() and simple to use may make it easy to produce basic graphs but may delay understanding philosophy of ggplot2 ggplot() # grammar of graphics plot – focus of this workshop provides fuller implementation of The Grammar of Graphics may have steeper learning curve but allows much more flexibility when building graphs 4 Grammar Defines Components of Graphics data: in ggplot2, data must be stored as an R data frame coordinate system: describes 2-D space that data is projected onto - for example, Cartesian coordinates, polar coordinates, map projections, ... geoms: describe type of geometric objects that represent data - for example, points, lines, polygons, ... aesthetics: describe visual characteristics that represent data - for example, position, size, color, shape, transparency, fill scales: for each aesthetic, describe how visual characteristic is converted to display values - for example, log scales, color scales, size scales, shape scales, .. -
Sharing and Organizing Research Products As R Packages Matti Vuorre1 & Matthew J
Sharing and organizing research products as R packages Matti Vuorre1 & Matthew J. C. Crump2 1 Oxford Internet Institute, University of Oxford, United Kingdom 2 Department of Psychology, Brooklyn College of CUNY, New York USA A consensus on the importance of open data and reproducible code is emerging. How should data and code be shared to maximize the key desiderata of reproducibility, permanence, and accessibility? Research assets should be stored persistently in formats that are not software restrictive, and documented so that others can reproduce and extend the required computations. The sharing method should be easy to adopt by already busy researchers. We suggest the R package standard as a solution for creating, curating, and communicating research assets. The R package standard, with extensions discussed herein, provides a format for assets and metadata that satisfies the above desiderata, facilitates reproducibility, open access, and sharing of materials through online platforms like GitHub and Open Science Framework. We discuss a stack of R resources that help users create reproducible collections of research assets, from experiments to manuscripts, in the RStudio interface. We created an R package, vertical, to help researchers incorporate these tools into their workflows, and discuss its functionality at length in an online supplement. Together, these tools may increase the reproducibility and openness of psychological science. Keywords: reproducibility; research methods; R; open data; open science Word count: 5155 Introduction package standard, with additional R authoring tools, provides a robust framework for organizing and sharing reproducible Research projects produce experiments, data, analyses, research products. manuscripts, posters, slides, stimuli and materials, computa- Some advances in data-sharing standards have emerged: It tional models, and more. -
Rkward: a Comprehensive Graphical User Interface and Integrated Development Environment for Statistical Analysis with R
JSS Journal of Statistical Software June 2012, Volume 49, Issue 9. http://www.jstatsoft.org/ RKWard: A Comprehensive Graphical User Interface and Integrated Development Environment for Statistical Analysis with R Stefan R¨odiger Thomas Friedrichsmeier Charit´e-Universit¨atsmedizin Berlin Ruhr-University Bochum Prasenjit Kapat Meik Michalke The Ohio State University Heinrich Heine University Dusseldorf¨ Abstract R is a free open-source implementation of the S statistical computing language and programming environment. The current status of R is a command line driven interface with no advanced cross-platform graphical user interface (GUI), but it includes tools for building such. Over the past years, proprietary and non-proprietary GUI solutions have emerged, based on internal or external tool kits, with different scopes and technological concepts. For example, Rgui.exe and Rgui.app have become the de facto GUI on the Microsoft Windows and Mac OS X platforms, respectively, for most users. In this paper we discuss RKWard which aims to be both a comprehensive GUI and an integrated devel- opment environment for R. RKWard is based on the KDE software libraries. Statistical procedures and plots are implemented using an extendable plugin architecture based on ECMAScript (JavaScript), R, and XML. RKWard provides an excellent tool to manage different types of data objects; even allowing for seamless editing of certain types. The objective of RKWard is to provide a portable and extensible R interface for both basic and advanced statistical and graphical analysis, while not compromising on flexibility and modularity of the R programming environment itself. Keywords: GUI, integrated development environment, plugin, R.