December 2016, Volume 34 No.2
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Analysis of Cell-Based Rnai Screens Comment Michael Boutros*, Lígia P Brás†‡ and Wolfgang Huber†
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Springer - Publisher Connector Open Access Software2006BoutrosetVolume al. 7, Issue 7, Article R66 Analysis of cell-based RNAi screens comment Michael Boutros*, Lígia P Brás†‡ and Wolfgang Huber† Addresses: *Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany. †EMBL - European Bioinformatics Institute, Cambridge CB10 1SD, UK. ‡Centre for Chemical and Biological Engineering, IST, Technical University of Lisbon, Av. Rovisco Pais, P-1049-001 Lisbon, Portugal. Correspondence: Michael Boutros. Email: [email protected]. Wolfgang Huber. Email: [email protected] reviews Published: 25 July 2006 Received: 27 March 2006 Revised: 7 June 2006 Genome Biology 2006, 7:R66 (doi:10.1186/gb-2006-7-7-r66) Accepted: 25 July 2006 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2006/7/7/R66 © 2006 Boutros et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. reports Analysis<p>cellHTS of cell-based is a new method RNAi screens for the analysis and documentation of RNAi screens.</p> Abstract RNA interference (RNAi) screening is a powerful technology for functional characterization of deposited research biological pathways. Interpretation of RNAi screens requires computational and statistical analysis techniques. We describe a method that integrates all steps to generate a scored phenotype list from raw data. -
A Word from Our 2006 Section Chairs
VOLUME 17, NO 1, JUNE 2006 A joint newsletter of the Statistical Computing & Statistical Graphics Sections of the American Statistical Association A Word from our 2006 Section Chairs PAUL MURRELL STEPHAN R. SAIN GRAPHICS COMPUTING I would like to begin by When Carey Priebe asked me highlighting a couple of to run for one of the section interesting recent offices a couple of years ago, I developments in the area of wasn’t exactly sure what I was Statistical Graphics. getting into. Now that I have There has been a lot of been chair for a couple of activity on the GGobi project months, I’m still not totally lately, with an updated web sure what I’ve gotten into. site, new versions, and The one thing I do know, improved links to R. I though, is that I’m very happy encourage you to (re)visit www.ggobi.org and see what to be involved in the section. they’ve been up to. There are a lot of very interesting things going on and, as always, a lot of opportunity for people who have an The third volume of the Handbook of Computational interest in statistical computing. Statistics, which is focused on Data Visualization, is scheduled for publication at the end of this year and Continues on Page 2.......... there will be a workshop as a satellite of Compstat 2006. This important volume will contain over 30 contributions and will provide a comprehensive overview of all areas of data visualization. Information about this project is available at gap.stat.sinica.edu.tw/ HBCSC. -
The Rattle Package September 30, 2007
The rattle Package September 30, 2007 Type Package Title A graphical user interface for data mining in R using GTK Version 2.2.64 Date 2007-09-29 Author Graham Williams <[email protected]> Maintainer Graham Williams <[email protected]> Depends R (>= 2.2.0) Suggests RGtk2, ada, amap, arules, bitops, cairoDevice, cba, combinat, doBy, e1071, ellipse, fEcofin, fCalendar, fBasics, foreign, fpc, gdata, gtools, gplots, Hmisc, kernlab, MASS, Matrix, mice, network, pmml, randomForest, rggobi, ROCR, RODBC, rpart, RSvgDevice, XML Description Rattle provides a Gnome (RGtk2) based interface to R functionality for data mining. The aim is to provide a simple and intuitive interface that allows a user to quickly load data from a CSV file (or via ODBC), transform and explore the data, and build and evaluate models, and export models as PMML (predictive modelling markup language). All of this with knowing little about R. All R commands are logged and available for the user, as a tool to then begin interacting directly with R itself, if so desired. Rattle also exports a number of utility functions and the graphical user interface does not need to be run to deploy these. License GPL version 2 or newer URL http://rattle.togaware.com/ R topics documented: audit . 2 calcInitialDigitDistr . 3 calculateAUC . 3 centers.hclust . 4 drawTreeNodes . 5 drawTreesAda . 6 evaluateRisk . 7 1 2 audit genPlotTitleCmd . 8 rattle_gui . 9 listRPartRules . 9 listTreesAda . 10 plotBenfordsLaw . 11 plotNetwork . 11 plotOptimalLine . 12 plotRisk . 14 printRandomForests . 16 randomForest2Rules . 17 rattle . 18 savePlotToFile . 19 treeset.randomForest . 19 Index 21 audit Sample dataset for illustration Rattle functionality. -
Uros2018.Pdf
Use of R in O cial Statistics 6th International Conference 2018 2018OV010 Eventbanner uRos2018 Rolbanner 100x200_DEF OPTIES .indd 1 23-7-2018 09:58:34 Eventbanner uRos2018 1920x400.jpg Eventbanner uRos2018 1920x400.bb Welcome The global community of R users is growing, and the number of Naonal and Interna- onal Stascal Offices that are adopng R is growing as well. About five years ago, when this conference was organized as an internaonal conference for the first me in Romania, we felt a bit like outlaws using Free and Open Source Soware (FOSS) in an area where commercial packages rule the land. How mes have changed: in the mean me FOSS, and in parcular R is considered a driving force of innovaon in academia, industry and government. The popularity of R is demonstrated by the hundreds of local R user groups, the thousands of R packages, and the RConsorum. The current conference, at Stascs Netherlands, marks the first occasion outside of the place where it was conceived: Romania. We are therefore especially pleased that our keynote speakers have roots in both countries. Alina Matei is a professor of stascs in Switzerland with Romanian roots. She will talk about opmal sample coordinaon using R. An important topic in mes where the reducon of response burden and increasing nonresponse rates force us to use smaller, more complex sampling methods. Not many R users are aware that there is a ‘touch of Dutch’ in R. Since 2017, Jeroen Ooms (UC Berkeley) is the maintainer of both Rtools and R for Windows. He will tell us about what it takes to compile, release, and modernize a system on which more than 12,500 R packages and millions of users rely every day. -
Statcharrms R Version Installation Guide
StatCharrms R Version Installation Guide 2014-07-14 Written and Programmed By: Joe Swintek, BTS Based off StatCharrms SAS version developed by: Dr. John Green, DuPont Applied Statistics Group, Stine-Haskell Research Center Additional Testing By: Kevin Flynn, USEPA Jon Haselman, USEPA Funded By: USEPA Under Contract EP-D-13-052 Installation StatCharrms is a graphical user interface front end for R, designed for ease of operation that performs the recommended statistical procedure used in the Medaka Extended One Generation Test (MEOGRT) and Larval Amphibian Growth and Development Assay (LAGDA). The statistical procedures implemented within StatCharrms are; the Rao-Scott adjusted Cochran-Armitage trend test by slices (RSCABS), a repeated measures ANVOA using time and treatment as fixed effects, Jonckheere-Terpstra trend test, Dunnett test, Kruskal Wallis, Dunns Test, one way ANOVA, weighted one way ANOVA, mixed effect ANOVA for imbalanced replicate structures, and a mixed effect Cox proportional model for imbalanced replicate structures. StatCharrms is implemented as an R workspace preloaded with the required functions. To Start StatCharrms double click on the R icon labeled StatCharrms-V##.RData. Now the installation of the required packages can begin by typing : Install.StatCharrms() into the R console and then hitting enter. R is case sensitive so you will need to type the command exactly as it is above. Figure one shows what is should look like. Executing the installation command will, by default, create a folder on the C drive called “RLib” that will contain the libraries needed for StatCharrms to run. Figure 1: Next a window asking to select CRAN (Comprehensive R Archive Network) mirror will popup. -
Sexy-Rgtk: a Package for Programming Rgtk2 GUI in a User-Friendly Manner
sexy-rgtk: a package for programming RGtk2 GUI in a user-friendly manner Damien Lerouxa and Nathalie Villa-Vialaneixa;b a INRA, UR875, MIAT F-31326 Castanet Tolosan - France [email protected] b SAMM, Université Paris 1 F-75634 Paris - France [email protected] Keywords: Gtk2, RGtk2, GUI There are many dierent ways to program Graphical User Interfaces (GUI) in R.[1] provides an overview of the available methods, describing ways to program R GUI with RGtk2, qtbase and tcltk. More recently, the package shiny, for building interactive web applications, was also released (the rst version has been published on December, 2012). The package RGtk2 [2] is probably one of the most complete packages to program complex and highly customizable GUI. It is based on GTK2 (the GIMP Toolkit, http://www.gtk. org/), which is a multi-platform toolkit for creating Graphical User Interfaces. GTK2 oers a complete set of widgets and can be used to develop complete application suites working on Linux, Windows and Mac OS X. Although very exible, each RGtk2 interface results in a long script that has a counterintuitive syntax for most R users. For instance, the simple window of Figure1 1 is obtained with the command lines provided in Figure2 (left). Figure 1: A simple GUI interface made with RGtk2. One attempt to overcome the diculty of the RGtk2 syntax is the package gWidgets but, quoting its reference manual The excellent RGtk2 package opens up the full power of the GTK2 toolkit, only a fraction of which is available though gWidgetsRGtk2. -
Pipenightdreams Osgcal-Doc Mumudvb Mpg123-Alsa Tbb
pipenightdreams osgcal-doc mumudvb mpg123-alsa tbb-examples libgammu4-dbg gcc-4.1-doc snort-rules-default davical cutmp3 libevolution5.0-cil aspell-am python-gobject-doc openoffice.org-l10n-mn libc6-xen xserver-xorg trophy-data t38modem pioneers-console libnb-platform10-java libgtkglext1-ruby libboost-wave1.39-dev drgenius bfbtester libchromexvmcpro1 isdnutils-xtools ubuntuone-client openoffice.org2-math openoffice.org-l10n-lt lsb-cxx-ia32 kdeartwork-emoticons-kde4 wmpuzzle trafshow python-plplot lx-gdb link-monitor-applet libscm-dev liblog-agent-logger-perl libccrtp-doc libclass-throwable-perl kde-i18n-csb jack-jconv hamradio-menus coinor-libvol-doc msx-emulator bitbake nabi language-pack-gnome-zh libpaperg popularity-contest xracer-tools xfont-nexus opendrim-lmp-baseserver libvorbisfile-ruby liblinebreak-doc libgfcui-2.0-0c2a-dbg libblacs-mpi-dev dict-freedict-spa-eng blender-ogrexml aspell-da x11-apps openoffice.org-l10n-lv openoffice.org-l10n-nl pnmtopng libodbcinstq1 libhsqldb-java-doc libmono-addins-gui0.2-cil sg3-utils linux-backports-modules-alsa-2.6.31-19-generic yorick-yeti-gsl python-pymssql plasma-widget-cpuload mcpp gpsim-lcd cl-csv libhtml-clean-perl asterisk-dbg apt-dater-dbg libgnome-mag1-dev language-pack-gnome-yo python-crypto svn-autoreleasedeb sugar-terminal-activity mii-diag maria-doc libplexus-component-api-java-doc libhugs-hgl-bundled libchipcard-libgwenhywfar47-plugins libghc6-random-dev freefem3d ezmlm cakephp-scripts aspell-ar ara-byte not+sparc openoffice.org-l10n-nn linux-backports-modules-karmic-generic-pae -
Annexes : Installation Du Logiciel R Et Des Packages R
Annexes : Installation du logiciel R et des packages R Pr´e-requis et objectif • Aucun pr´e-requis n’est n´ecessaire.La lecture du chapitre 1 pourrait tou- tefois se r´ev´eler int´eressante. • Ce chapitre d´ecritcomment installer le logiciel R, dans sa version x (rem- placer partout dans le reste de ce document x par le num´ero de la derni`ere version disponible), sous le syst`emed’exploitation Microsoft Windows et aussi comment ajouter des packages suppl´ementaires sous Windows ou sous Linux. SECTION C.1 Installation de R sous Microsoft Windows Commencez par t´el´echarger le logiciel R (fichier R-x-win.exe o`u x est le nu- m´ero de la derni`ereversion disponible) `a l’aide de votre navigateur web usuel `a l’adresse suivante : http://cran.r-project.org/bin/windows/base/ Enregistrez ensuite ce fichier ex´ecutable sur le bureau de Windows puis double- cliquez sur le fichier R-x-win.exe dont voici l’icˆone : . Le logiciel s’installe alors et vous n’avez plus qu’`a suivre les instructions qui s’affichent et `a conserver les options propos´ees par d´efaut. Lorsque l’icˆone est ajout´ee sur le bureau, l’installation peut ˆetre consi- d´er´ee comme termin´ee. 574 Le logiciel R SECTION C.2 Installation de packages suppl´ementaires De nombreux modules (packages ou librairies) suppl´ementaires sont dispo- nibles sur le site internet : http://cran.r-project.org/web/packages/available_packages_by_name. html, ou bien encore ici : http://cran.r-project.org/bin/windows/contrib/, dans le dossier corres- pondant au num´ero x de votre version de R. -
Une Interface Graphique Pour Analyser Des Données Distantes Sous R
Accéder aux données Des méthodes d'analyse dans une interface graphique Application à des mesures biologiques Perspectives et limites Une interface graphique pour analyser des données distantes sous R Raphaël Coudret(1), Gilles Durrieu(2), Jérôme Saracco(1) (1)Équipe CQFD, INRIA Bordeaux - Sud-Ouest et IMB, Université de Bordeaux (2)LMBA, Université de Bretagne Sud 1ères Rencontres R, 2 Juillet 2012, Bordeaux Les packages RMySQL et RGtk2 Coudret, Durrieu, Saracco 1/15 Accéder aux données Des méthodes d'analyse dans une interface graphique Application à des mesures biologiques Perspectives et limites Sommaire Accéder aux données Les fonctionnalités de MySQL Utiliser des commandes SQL sous R Des méthodes d'analyse dans une interface graphique Les fenêtres et les boutons de Gtk+ ... ... disponibles sous R Application à des mesures biologiques Contexte Un estimateur de densité particulier Les packages RMySQL et RGtk2 Coudret, Durrieu, Saracco 2/15 Accéder aux données Accéder aux données Des méthodes d'analyse dans une interface graphique Les fonctionnalités de MySQL Application à des mesures biologiques Utiliser des commandes SQL sous R Perspectives et limites Les fonctionnalités de MySQL I Mise en ordre de grands jeux de données ! Tables, bases, index I Connexion sécurisée à la base de données ! Droits de lecture, d'écriture, de création de tables I Interopérabilité ! Systèmes d'exploitation, langages de programmation Exploitation des données, travail en groupe, diusion de résultats Les packages RMySQL et RGtk2 Coudret, Durrieu, Saracco -
NAMJOSHI-DISSERTATION-2017.Pdf
Copyright by Sanjeev Vinayak Namjoshi 2017 The Dissertation Committee for Sanjeev Vinayak Namjoshi Certifies that this is the approved version of the following dissertation: Bioinformatic Approaches to Screening the Molecular Framework Underlying Local Dendritic mRNA Translation Committee: Johann Hofmann Supervisor Kimberly F. Raab-Graham Co- Supervisor Nigel S. Atkinson Edward M. Marcotte Christopher S. Sullivan Bioinformatic Approaches to Screening the Molecular Framework Underlying Local Dendritic mRNA Translation by Sanjeev Vinayak Namjoshi, B.S.Bio Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin May 2017 Dedication I dedicate this work to all those who have been patient and supportive of me for over half a decade. To Dr. Kimberly Raab-Graham for her guidance and vision which has nurtured me into the scientist I am today. To the Raab-Graham lab for listening to my rambling discourse, bad music, and being a clarifying force in moments of confusion. To my mother for her unending supply of wisdom and council so I could better understand myself. To my father for questioning my own assumptions so that I could become a better scientist. To my sister for helping me realize what it is I believe. To my friends: Ariana, Alex & Alex, Jennifer, Kalen, Leslie, Peter, and Rick, who always inquired about my progress and emboldened me to move forward. To Elissa Jo for her constant encouragement and unwavering optimism at the most difficult moments. Finally, I dedicate the following quote to all the rodents whose heads have been sacrificed for my projects: “The world to which we have belonged offers nothing to love outside of each individual insufficiency: its existence is limited to utility […] Existence is not only an agitated void, it is a dance that forces one to dance with fanaticism. -
Univerzita Pardubice Fakulta Elektrotechniky a Informatiky Porovnání Grafických Knihoven Na Vestavěném Zařízení Jan Ší
Univerzita Pardubice Fakulta elektrotechniky a informatiky Porovnání grafických knihoven na vestavěném zařízení Jan Šíma Bakalářská práce 2009 Prohlášení autora Prohlašuji: Tuto práci jsem vypracoval samostatně. Veškeré literární prameny a informace, které jsem v práci využil, jsou uvedeny v seznamu použité literatury. Byl jsem seznámen s tím, že se na moji práci vztahují práva a povinnosti vyplývající ze zákona č. 121/2000 Sb., autorský zákon, zejména se skutečností, že Univerzita Pardubice má právo na uzavření licenční smlouvy o užití této práce jako školního díla podle § 60 odst. 1 autorského zákona, a s tím, že pokud dojde k užití této práce mnou nebo bude poskytnuta licence o užití jinému subjektu, je Univerzita Pardubice oprávněna ode mne požadovat přiměřený příspěvek na úhradu nákladů, které na vytvoření díla vynaložila, a to podle okolností až do jejich skutečné výše. Souhlasím s prezenčním zpřístupněním své práce v Univerzitní knihovně. V Pardubicích dne 29. 4. 2009 Jan Šíma Poděkování Na této stránce, která je učená pro poděkování, bych chtěl poděkovat hlavně Mgr. Tomáši Hudcovi, který mi velmi pomohl při zpracování bakalářské práce. Dále bych chtěl poděkovat Jarmile Šímové při pomoci s opravou českého pravopisu. Dále Ing. Janu Kroulíkovi, „embedded Linux developerovi“, ze společnosti MIKRO- ELEKTRONIKA spol. s r. o.. Všem zmíněným děkuji za pomoc při mé práci. Anotace a klíčová slova Anotace Práce je věnována paměťové a časové náročnosti grafických knihoven pro X Window se zaměřením na multiplatformní knihovny. Věnuje se knihovnám Qt, GTK+, wxWidgets, FLTK, Fast Toolkit. Zabývá se jejich porovnáním mezi sebou a následnému testování jednotlivých knihoven. Klíčová slova GTK+, Qt, FLTK, wxWidgets, Fast Toolkit, grafické knihovny, paměť, čas, Unix, RAM TITLE Comparison of graphic libraries for embedded device ANNOTATION This work is dedicated to measure the memory and time performance of graph- ics libraries for X Window with a focus on multi-platform library. -
Bioconductor Annual Report 2011
Bioconductor Annual Report 2011 Martin Morgan Fred Hutchinson Cancer Research Center July 2011 Contents 1 Project Scope1 1.1 Packages................................1 1.2 Courses and Conferences.......................2 1.3 Community..............................3 1.4 Publication..............................3 1.5 Funding................................4 2 Core Tasks & Capabilities5 2.1 Automated Package Building and Testing.............5 2.2 Package submission management..................5 2.3 Annotation data package building..................6 2.4 Other Tasks..............................6 2.5 Hardware...............................6 2.6 Key Personnel.............................6 A Appendix: Proposal Specific Aims 11 1 Project Scope Bioconductor provides access to software for the analysis and comprehension of high throughput genomic data. Packages are written in the R programming lan- guage by members of the Bioconductor team and the international community. Bioconductor was started approximately 10 years ago (Fall, 2001) by Dr. Robert Gentleman and others, and now consists of >460 packages for the analysis of data ranging from expression microarrays through next-generation sequencing. 1.1 Packages R software packages represent the primary product of the Bioconductor project. Packages are produced by the Bioconductor team or are from international con- tributors. Table1 summarizes growth in the number of packages hosted by 1 Table 1: Number of contributed packages included in each Bioconductor release. Releases occur twice per year. Release N Release N Release N 2002 1.0 15 2006 1.8 172 2010 2.6 389 1.1 20 1.9 188 2.7 419 2003 1.2 30 2007 2.0 214 2011 2.8 467 1.3 49 2.1 233 2004 1.4 81 2008 2.2 260 1.5 100 2.3 294 2005 1.6 123 2009 2.4 320 1.7 141 2.5 352 Bioconductor, with 467 packages available in the current release.