Spotter Documentation Version 0.5, Released 4/12/2010
|
|
- Amos Parker
- 5 years ago
- Views:
Transcription
1 Spotter Documentation Version 0.5, Released 4/12/2010 Purpose Spotter is a program for delineating an association signal from a genome wide association study using features such as recombination rates, genetic distance, linkage disequilibrium, and association p values. Requirements A program for calculating LD information called new_fugue, written by Goncalo Abecasis. It can be downloaded from: Python version 2.5 (or greater) and less than 3.0. Python 3 is a separate and incompatible branch. Synopsis Typical usage of Spotter: spotter --metal association_results_file.txt --snplist rs1,rs2,rs3 If you have a file that already contains a list of SNPs, you can do the following: spotter --metal association_results_file.txt --hits file_with_snps.txt Spotter will parse out the rs### SNPs from that file and run the algorithm on each one. Installation Spotter is ready to run out of the box, as long as new_fugue and a Python interpreter are already installed on your system. We provide as a starting point: HapMap phase II CEU build 36 genotype files, for computing LD information HapMap recombination rates, build 36 HapMap genetic map, build 36 UCSC refflat table (gene information), build 36 UCSC sequence gap table, build 36 These various pieces of data can be changed by the user. Configuration Users will likely wish to supply their own data. To change the data that Spotter uses, the user can edit the conf/config.xml file. Data sources listed under required_data can be provided by the user. Sources listed under created_data must be created by running bin/setup.py, a script for downloading and formatting data from the UCSC database. Input Spotter requires 2 pieces of information to run: a file containing association results, and a list of SNPs to use for defining regions.
2 The association results file should look like the following (note, the following is just an example): snp chr pos p value rs e 04 Each row should be a SNP, with its chromosome, position, and p value (from GWAS or meta analysis). Please take care to provide SNP positions that are from the same build as the HapMap and UCSC files provided with Spotter (build 36 / hg18.) The file should be tab delimited. SNPs can be provided by using either the snplist option, or the hits option (see Options section below.) Options Argument Description General program options o, out <file> cache <file> Specify output file for report. Spotter attempts to create two files one containing the identified intervals, and one containing information on each gene found within those intervals. For example, if you specify: out my_project.txt Spotter will create the following two report files: my_project_intervals.txt my_project_genes.txt Change the location of the LD cache file. Spotter caches LD on each run of the program so that it only needs to be computed once per locus. This greatly speeds up additional runs of the program. The default location is to create a file called ld_cache.db in the current directory. Options for specifying SNPs snplist <string> Run algorithm for each SNP in this list. The list must be specified in quotes, separated by commas. Example: snplist rs1,rs2,rs3 hits <file> Run algorithm for each SNP present in this file. Spotter attempts to pattern match rs### identifiers from the file. Options for specifying association results metal <file> delim <character> Association results file. See the section on Input for more information about the format of this file. The delimiter of the association results file. Defaults to tab. Options for specifying algorithm method <string> Specify which algorithm Spotter should use. Currently only a sliding window method
3 is supported. See section on algorithms below for more information. Options for sliding window method slw_pval <float> P value threshold for sliding window method. This should be specified as a raw p value, and not a log transformed one. slw_usepval Disable using p values for sliding window. Default is True i.e., do not use p values. This should be enabled with caution, especially if running over many different loci. P values scales are often very different for each locus. slw_r2 <float> LD (r^2) threshold. Default is 0.5. slw_ratethresh <float> Recombination rate threshold, in cm/mb units. Default is 10. slw_winsize <int> slw_userate Sliding window size, in bases. Default is 75,000 bases (75 KB). Toggles using recombination rates instead of genetic distance. slw_cmdist <float> Genetic distance to travel beyond the LD interval, in cm. Default is slw_usecm Toggles using genetic map distance. This is the default. Output Spotter creates two output files: one containing intervals identified by the algorithm, the other containing information on genes within each interval. See out" for controlling the names of these output files. Algorithm Sliding window method Spotter s primary algorithm uses a sliding window approach. Within each window, the algorithm checks to see if a SNP exceeds either the p value threshold, or the LD threshold. If at least one SNP within the window exceeds either of these thresholds, the window slides forward, and tries the same procedure again until failure. Once a window is found that does not contain a SNP exceeding either the p value or LD threshold, the algorithm stops scanning. It then finds the last best SNP i.e. the last SNP to pass the LD or p value threshold, and expands beyond this point until either 1) the nearest recombination peak, or 2) a specified genetic distance. The figure below shows how the algorithm works as it scans to the right from the index SNP (in this case, we choose the index SNP as the best p value in the region.) For this example, we use the following settings: P value threshold: 1E 05 ( slw_pval 1e 05, slw_usepval) LD threshold: r^2 > 0.4 ( slw_r2 0.5) Recombination peak: cm/mb > 10 ( slw_ratethresh 10, slw_userate) Sliding window size: 75 kilobases ( slw_winsize 75000) Here, we ve chosen a particular locus, and want to identify the interval near the index SNP. We start by scanning to the right of the index SNP: Window 1: succeeds, since SNPs underneath the window exceed both p value and LD threshold Window 2: succeeds, since SNPs underneath the window are exceeding the LD threshold Window 3: fails, no SNPs above p value or LD threshold
4 The last SNP to exceed either the p value or LD threshold is shown with a red arrow. From here, we scan to the right to find the nearest recombination peak, shown with a blue arrow (it s actually quite difficult to see here, you may need to zoom in!) This exact same procedure would also be repeated to scan to the left of the index SNP (not shown here.) The interval detected in this example is shown by two black lines (or the highlighted blue region in the gene track.) Figure a visual overview of how the sliding window algorithm detects an association signal interval. The plot shows association results from a GWAS or meta analysis of GWAS studies. Each point is a SNP, colored by its LD (r 2 ) value with the index SNP. The x axis is genomic position, and the y axis is the log 10 of the association p value. Visualizing Results Plots such as the one in the figure above can be created by using our software at: The interval selected by Spotter can be plotted using the Highlight Region of Interest feature under Plot Using Your Data section, or by supplying histart=# and hiend=# parameters under the Plots Using Your Data And Your Hitspec File batch mode section. Licensing Spotter is written by Ryan Welch (welchr@umich.edu) and is copyrighted by the University of Michigan. This software is licensed under the MIT free software license: Copyright (c) 2010, The University of Michigan Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be
5 included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
git-pr Release dev2+ng5b0396a
git-pr Release 0.2.1.dev2+ng5b0396a Mar 20, 2017 Contents 1 Table Of Contents 3 1.1 Installation................................................ 3 1.2 Usage...................................................
More informationX Generic Event Extension. Peter Hutterer
X Generic Event Extension Peter Hutterer X Generic Event Extension Peter Hutterer X Version 11, Release 7.7 Version 1.0 Copyright 2007 Peter Hutterer Permission is hereby granted, free of charge, to any
More informationThe above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
1. License The MIT License (MIT) Copyright (c) 2018 gamedna Ltd Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"),
More informationFeed Cache for Umbraco Version 2.0
Feed Cache for Umbraco Version 2.0 Copyright 2010, Ferguson Moriyama Limited. All rights reserved Feed Cache for Umbraco 2.0 Page 1 Introduction... 3 Prerequisites... 3 Requirements... 3 Downloading...
More informationSensor-fusion Demo Documentation
Sensor-fusion Demo Documentation Release 1.2 Alexander Pacha Aug 13, 2018 Contents: 1 Euler Angles 3 2 Installation 5 3 Contribute 7 4 License 9 i ii Sensor-fusion Demo Documentation, Release 1.2 This
More informationThe above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
Simple Robot Simulator 2010 (SRS10) Written by Walter O. Krawec Copyright (c) 2013 Walter O. Krawec Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
More informationmp3fm Documentation Release Akshit Agarwal
mp3fm Documentation Release 1.0.1 Akshit Agarwal July 27, 2013 CONTENTS 1 Introduction to MP3fm 3 1.1 Features.................................................. 3 2 Libraries Used and Install 5 2.1 Libraries
More informationutidylib Documentation Release 0.4
utidylib Documentation Release 0.4 Michal Čihař Nov 01, 2018 Contents 1 Installing 3 2 Contributing 5 3 Running testsuite 7 4 Building documentation 9 5 License 11 6 Changes 13 6.1 0.5....................................................
More informationAsthma Eliminator MicroMedic Competition Entry
Asthma Eliminator 2013 MicroMedic Competition Entry Overview: Our project helps people with asthma to avoid having asthma attacks. It does this by monitoring breath pressure and alerting the user if the
More informationElegans Documentation
Elegans Documentation Release 0.1.0 Naoki Nishida April 29, 2014 Contents i ii CHAPTER 1 Description Elegans is a 3D plotting library written in JavaScript. With Elegans, you can generate charts in JavaScript,
More informationGenetic Analysis. Page 1
Genetic Analysis Page 1 Genetic Analysis Objectives: 1) Set up Case-Control Association analysis and the Basic Genetics Workflow 2) Use JMP tools to interact with and explore results 3) Learn advanced
More informationdeepatari Documentation
deepatari Documentation Release Ruben Glatt July 29, 2016 Contents 1 Help 3 1.1 Installation guide............................................. 3 2 API reference 5 2.1 Experiment Classes........................................
More informationDellve CuDNN Documentation
Dellve CuDNN Documentation Release 1.0.0 DELLveTeam May 02, 2017 Contents 1 Install Requirements 3 2 Dellve CuDNN Framework 5 3 Dellve CuDNN Operations 7 4 API Reference 11 5 Contributing 13 6 Licensing
More informationMCAFEE THREAT INTELLIGENCE EXCHANGE RESILIENT THREAT SERVICE INTEGRATION GUIDE V1.0
MCAFEE THREAT INTELLIGENCE EXCHANGE RESILIENT THREAT SERVICE INTEGRATION GUIDE V1.0 Copyright IBM Corporation 2018 Permission is hereby granted, free of charge, to any person obtaining a copy of this software
More informationsensor-documentation Documentation
sensor-documentation Documentation Release 0.0.1 Apoorv Jagtap October 15, 2016 Contents 1 Contents: 1 1.1 Introduction............................................... 1 1.2 Velodyne VLP - 16............................................
More informationRTI Connext DDS Core Libraries
RTI Connext DDS Core Libraries Getting Started Guide Addendum for Database Setup Version 5.3.1 2018 Real-Time Innovations, Inc. All rights reserved. Printed in U.S.A. First printing. February 2018. Trademarks
More informationGWAS Exercises 3 - GWAS with a Quantiative Trait
GWAS Exercises 3 - GWAS with a Quantiative Trait Peter Castaldi January 28, 2013 PLINK can also test for genetic associations with a quantitative trait (i.e. a continuous variable). In this exercise, we
More informationTWO-FACTOR AUTHENTICATION Version 1.1.0
TWO-FACTOR AUTHENTICATION Version 1.1.0 User Guide for Magento 1.9 Table of Contents 1..................... The MIT License 2.................... About JetRails 2FA 4................. Installing JetRails
More informationBME280 Documentation. Release Richard Hull
BME280 Documentation Release 0.2.1 Richard Hull Mar 18, 2018 Contents 1 GPIO pin-outs 3 1.1 P1 Header................................................ 3 2 Pre-requisites 5 3 Installing the Python Package
More informationExaFMM. Fast multipole method software aiming for exascale systems. User's Manual. Rio Yokota, L. A. Barba. November Revision 1
ExaFMM Fast multipole method software aiming for exascale systems User's Manual Rio Yokota, L. A. Barba November 2011 --- Revision 1 ExaFMM User's Manual i Revision History Name Date Notes Rio Yokota,
More informationOpen Source Used In Cisco Configuration Professional for Catalyst 1.0
Open Source Used In Cisco Configuration Professional for Catalyst 1.0 Cisco Systems, Inc. www.cisco.com Cisco has more than 200 offices worldwide. Addresses, phone numbers, and fax numbers are listed on
More informationInptools Manual. Steffen Macke
Inptools Manual Steffen Macke Inptools Manual Steffen Macke Publication date 2014-01-28 Copyright 2008, 2009, 2011, 2012, 2013, 2014 Steffen Macke Permission is granted to copy, distribute and/or modify
More informationFirebase PHP SDK. Release
Firebase PHP SDK Release Jul 16, 2016 Contents 1 User Guide 3 1.1 Overview................................................. 3 1.2 Authentication.............................................. 3 1.3 Retrieving
More informationaiounittest Documentation
aiounittest Documentation Release 1.1.0 Krzysztof Warunek Sep 23, 2017 Contents 1 What? Why? Next? 1 1.1 What?................................................... 1 1.2 Why?...................................................
More informationPyCon APAC 2014 Documentation
PyCon APAC 2014 Documentation Release 2014-01-12 Keith Yang July 06, 2014 Contents 1 PyCon APAC 2014 3 1.1 Getting Started.............................................. 3 1.2 Setting up the database..........................................
More informationTailor Documentation. Release 0.1. Derek Stegelman, Garrett Pennington, and Jon Faustman
Tailor Documentation Release 0.1 Derek Stegelman, Garrett Pennington, and Jon Faustman August 15, 2012 CONTENTS 1 Quick Start 3 1.1 Requirements............................................... 3 1.2 Installation................................................
More informationXEP-0099: IQ Query Action Protocol
XEP-0099: IQ Query Action Protocol Iain Shigeoka mailto:iain@jivesoftware.com xmpp:smirk@jabber.com 2018-11-03 Version 0.1.1 Status Type Short Name Deferred Standards Track Not yet assigned Standardizes
More informationDaedalus Documentation
Daedalus Documentation Release 0.1.0 Joshua Estes Sep 27, 2017 Contents 1 Installation 3 1.1 With Composer.............................................. 3 1.2 Global Install with Composer......................................
More informationXEP-0087: Stream Initiation
XEP-0087: Stream Initiation Thomas Muldowney mailto:temas@jabber.org xmpp:temas@jabber.org 2003-05-22 Version 0.1 Status Type Short Name Retracted Standards Track si A common method to initiate a stream
More informationSopaJS JavaScript library package
SopaJS JavaScript library package https://staff.aist.go.jp/ashihara-k/sopajs.html AIST August 31, 2016 1 Introduction SopaJS is a JavaScript library package for reproducing panoramic sounds on the Web
More informationFolder Poll General User s Guide
Document version 11 Product Release version 3.0 Folder Poll General User s Guide MyAssays Ltd. 2016 www.myassays.com Contents Trademarks... 4 Copyright... 4 Additional Software Licensing Notices... 5 Online
More informationagate-sql Documentation
agate-sql Documentation Release 0.5.3 (beta) Christopher Groskopf Aug 10, 2017 Contents 1 Install 3 2 Usage 5 3 API 7 3.1 Authors.................................................. 8 3.2 Changelog................................................
More informationPHP-FCM Documentation
PHP-FCM Documentation Release 0.0.1 Edwin Hoksberg Apr 09, 2018 Contents 1 Overview 3 1.1 Requirements............................................... 3 1.2 Running the tests.............................................
More informationNTLM NTLM. Feature Description
Feature Description VERSION: 6.0 UPDATED: JULY 2016 Copyright Notices Copyright 2002-2016 KEMP Technologies, Inc.. All rights reserved.. KEMP Technologies and the KEMP Technologies logo are registered
More informationinflection Documentation
inflection Documentation Release 0.3.1 Janne Vanhala Oct 29, 2018 Contents 1 Installation 3 2 Contributing 5 3 API Documentation 7 4 Changelog 11 4.1 0.3.1 (May 3, 2015)...........................................
More informationGuest Book. The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
License Guest Book Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction,
More informationXTEST Extension Library
Version 2.2 XConsortium Standard Kieron Drake UniSoft Ltd. Copyright 1992 by UniSoft Group Ltd. Permission to use, copy, modify, and distribute this documentation for any purpose and without fee is hereby
More informationIndustries Package. TARMS Inc.
Industries Package TARMS Inc. September 07, 2000 TARMS Inc. http://www.tarms.com Copyright cfl2000 TARMS Inc. Permission is hereby granted, free of charge, to any person obtaining a copy of this model
More informationdublincore Documentation
dublincore Documentation Release 0.1.1 CERN Mar 25, 2018 Contents 1 User s Guide 3 1.1 Installation................................................ 3 1.2 Usage...................................................
More informationStep-by-Step Guide to Basic Genetic Analysis
Step-by-Step Guide to Basic Genetic Analysis Page 1 Introduction This document shows you how to clean up your genetic data, assess its statistical properties and perform simple analyses such as case-control
More informationClassPad Manager Subscription
For ClassPad II Series E ClassPad Manager Subscription (for Windows ) User s Guide CASIO Education website URL http://edu.casio.com Access the URL below and register as a user. http://edu.casio.com/dl/
More informationdisspcap Documentation
disspcap Documentation Release 0.0.1 Daniel Uhricek Dec 12, 2018 Installation 1 Requirements 3 1.1 Build depedencies............................................ 3 1.2 Python depedencies...........................................
More informationMEAS HTU21D PERIPHERAL MODULE
MEAS HTU21D PERIPHERAL MODULE Digital Humidity and Temperature Digital Component Sensor (DCS) Development Tools The HTU21D peripheral module provides the necessary hardware to interface the HTU21D digital
More informationPreprocessing of fmri data
Preprocessing of fmri data Pierre Bellec CRIUGM, DIRO, UdM Flowchart of the NIAK fmri preprocessing pipeline fmri run 1 fmri run N individual datasets CIVET NUC, segmentation, spatial normalization slice
More informationVMware vcenter Log Insight Manager. Deployment Guide
VMware vcenter Log Insight Manager Deployment Guide VERSION: 6.0 UPDATED: JULY 2016 Copyright Notices Copyright 2002-2016 KEMP Technologies, Inc.. All rights reserved.. KEMP Technologies and the KEMP Technologies
More informationInstagram PHP Documentation
Instagram PHP Documentation Release 0.1.0 Marvin Osswald Feb 12, 2018 Contents 1 Overview 3 1.1 Requirements............................................... 3 1.2 Installation................................................
More informationColgate, WI
Lions International District 27-A2 Technology Chair Lion Bill Meyers W290N9516 Deer Lane, Colgate, WI 53017 262.628.2940 27A2Tech@gmail.com Following is an explanation of the design basic of the free Lions
More informationTenable Hardware Appliance Upgrade Guide
Tenable Hardware Appliance Upgrade Guide June 4, 2012 (Revision 3) The newest version of this document is available at the following URL: http://static.tenable.com/prod_docs/tenable_hardware_appliance_upgrade.pdf
More informationImporting and Merging Data Tutorial
Importing and Merging Data Tutorial Release 1.0 Golden Helix, Inc. February 17, 2012 Contents 1. Overview 2 2. Import Pedigree Data 4 3. Import Phenotypic Data 6 4. Import Genetic Data 8 5. Import and
More informationUser Guide. Calibrated Software, Inc.
User Guide Calibrated Software, Inc. Copyright 2008 Calibrated Software, Inc. All rights reserved. www.calibratedsoftware.com Your rights to the software are governed by the accompanying Software License
More informationabstar Documentation Release Bryan Briney
abstar Documentation Release 0.3.1 Bryan Briney Apr 26, 2018 Contents 1 Getting Started 3 2 Usage 7 3 About 13 4 Related Projects 15 5 Index 17 i ii AbStar is a core component of the Ab[x] Toolkit for
More informationclipbit Release 0.1 David Fraser
clipbit Release 0.1 David Fraser Sep 27, 2017 Contents 1 Introduction to ClipBit 1 1.1 Typing in Programs........................................... 1 2 ClipBit Programs 2 2.1 Secret Codes...............................................
More informationPacket Trace Guide. Packet Trace Guide. Technical Note
Packet Trace Guide Technical Note VERSION: 2.0 UPDATED: JANUARY 2016 Copyright Notices Copyright 2002-2016 KEMP Technologies, Inc.. All rights reserved.. KEMP Technologies and the KEMP Technologies logo
More informationPyDotPlus Documentation
PyDotPlus Documentation Release 2.0.2 PyDotPlus Developers Sep 12, 2017 Contents 1 Quick Guide 3 2 API Reference 5 2.1 API Reference.............................................. 5 2.1.1 GraphViz Module........................................
More informationHTNG Web Services Product Specification. Version 2014A
HTNG Web Services Product Specification Version 2014A About HTNG Hotel Technology Next Generation (HTNG) is a non-profit association with a mission to foster, through collaboration and partnership, the
More informationXTEST Extension Protocol
Version 2.2 XConsortium Standard Kieron Drake UniSoft Ltd. Copyright 1992 by UniSoft Group Ltd. Permission to use, copy, modify, and distribute this documentation for any purpose and without fee is hereby
More informationMEAS TEMPERATURE SYSTEM SENSOR (TSYS01) XPLAINED PRO BOARD
MEAS TEMPERATURE SYSTEM SENSOR (TSYS01) XPLAINED PRO BOARD Digital Temperature Digital Component Sensor (DCS) Development Tools Performance -5 C to 50 C accuracy: 0.1 C -40 C to 125 C accuracy: 0.5 C Very
More informationTestworks User Guide. Release 1.0. Dylan Hackers
Testworks User Guide Release 1.0 Dylan Hackers April 10, 2019 CONTENTS 1 Testworks Usage 1 1.1 Quick Start................................................ 1 1.2 Defining Tests..............................................
More informationTransparency & Consent Framework
Transparency & Consent Framework Consent Manager Provider JS API v1.0 Table of Contents Introduction... 2 About the Transparency & Consent Framework... 2 About the Transparency & Consent Standard... 3
More informationNDIS Implementation Guide
NDIS Implementation Guide Last Update: February 2016 Interactive Reporting Pty Ltd ABN 68 128 589 266 8/248 Miller Street NORTH SYDNEY NSW 2060 Ph: (61 2) 8011 1511 Email: info@bi4cloud.com Website: www.bi4cloud.com
More informationjosync Documentation Release 1.0 Joel Goop and Jonas Einarsson
josync Documentation Release 1.0 Joel Goop and Jonas Einarsson May 10, 2014 Contents 1 Contents 3 1.1 Getting started.............................................. 3 1.2 Jobs....................................................
More informationJava Relying Party API v1.0 Programmer s Guide
Java Relying Party API v1.0 Programmer s Guide 4 June 2018 Authors: Peter Höbel peter.hoebel@open-xchange.com Vittorio Bertola vittorio.bertola@open-xchange.com This document is copyrighted by the ID4me
More informationUser s Guide for macos with Stata and R
User s Guide for macos with Stata and R Table of Contents Introduction... 4 Setup... 4 Basics of StatTag... 4 3.1 StatTag Elements... 5 3.2 Navigating StatTag for macos... 6 3.3 Interacting with the StatTag
More informationInternational Color Consortium
International Color Consortium Document ICC.1A:1999-04 Addendum 2 to Spec. ICC.1:1998-09 NOTE: This document supersedes and subsumes Document ICC.1A:1999-02, Addendum 1 to Spec ICC.1:1998-09 Copyright
More informationLANDISVIEW Beta v1.0-user Guide
LANDISVIEW Beta v1.0 User Guide Andrew G. Birt Lei Wang Weimin Xi Knowledge Engineering Laboratory (KEL) Texas A&M University Last Revised: November 27, 2006 1 Table of Contents 1. Introduction 2. Installation
More informationBICF Nano Course: GWAS GWAS Workflow Development using PLINK. Julia Kozlitina April 28, 2017
BICF Nano Course: GWAS GWAS Workflow Development using PLINK Julia Kozlitina Julia.Kozlitina@UTSouthwestern.edu April 28, 2017 Getting started Open the Terminal (Search -> Applications -> Terminal), and
More informationMatPlotTheme Documentation
MatPlotTheme Documentation Release 0.1.2 James Yu July 31, 2014 Contents 1 Contents 3 1.1 Overview................................................. 3 1.2 Gallery..................................................
More informationpuppet-diamond Documentation
puppet-diamond Documentation Release 0.3.0 Ian Dennis Miller Mar 21, 2017 Contents 1 Overview 3 2 Introduction 5 3 User Guide 9 4 About 15 i ii Puppet-Diamond is framework for creating and managing an
More informationdelegator Documentation
delegator Documentation Release 1.0.1 Daniel Knell August 25, 2014 Contents 1 Getting Started 3 1.1 Installation................................................ 3 1.2 Quickstart................................................
More informationHTNG Web Services Product Specification. Version 2011A
HTNG Web Services Product Specification Version 2011A About HTNG Hotel Technology Next Generation ( HTNG ) is a nonprofit organization with global scope, formed in 2002 to facilitate the development of
More informationDjango Mail Queue Documentation
Django Mail Queue Documentation Release 3.1.0 Derek Stegelman Jan 27, 2018 Contents 1 Quick Start Guide 3 1.1 Requirements............................................... 3 1.2 Installation................................................
More informationTransparency & Consent Framework
Transparency & Consent Framework Cookie and Vendor List Format v1.0a Table of Contents Introduction... 2 About the Transparency & Consent Framework... 2 About the Transparency & Consent Standard... 3 License...
More informationStatsd Metrics Documentation
Statsd Metrics Documentation Release 1.0.0 Farzad Ghanei Aug 05, 2018 Contents 1 Metrics 3 1.1 metrics Metric classes and helper functions............................ 4 2 Client 7 2.1 client Statsd client.........................................
More informationThe XIM Transport Specification
The XIM Transport Specification Revision 0.1 Takashi Fujiwara, FUJITSU LIMITED The XIM Transport Specification: Revision 0.1 by Takashi Fujiwara X Version 11, Release 7 Copyright 1994 FUJITSU LIMITED Copyright
More informationDATAGATE MK2. Box Contents. Additional Features (licenses) Features. Safety
DATAGATE MK2 Box Contents Datagate Mk2 (pn: 70044) Straight connect Ethernet lead (pn:79102) IEC power cord (country dependent plug) This User manual Features 8 DMX ports isolated up to 1500V Gigabit Ethernet
More informationUse in High-Safety Applications
------ ScanSnap Organizer V5.5L31 README File ------ - Contents - 1. Cautions for using environment-dependent characters 2. Cautions Concerning Installation 3. Cautions Concerning the Operation 4. Connecting
More informationCuteFlow-V4 Documentation
CuteFlow-V4 Documentation Release 4.0.0 Timo Haberkern Nov 15, 2017 Contents 1 Contributing 3 1.1 Contributing Code............................................ 3 1.2 Contributing Documentation.......................................
More informationImagination Documentation
Imagination Documentation Release 1.5 Juti Noppornpitak July 01, 2013 CONTENTS i ii Copyright Juti Noppornpitak Author Juti Noppornpitak License MIT Imagination
More informationmqtt-broker Documentation
mqtt-broker Documentation Release 1 Tegris April 09, 2016 Contents 1 Table of Contents 3 1.1 Getting Started.............................................. 4 1.2 Frontend Console.............................................
More informationBlack Mamba Documentation
Black Mamba Documentation Release 1.4.3 Robert Vojta Jan 11, 2018 Contents 1 About Black Mamba 3 2 Black Mamba User Guide 5 3 Black Mamba Reference 15 4 Contribution 25 5 Development 27 6 FAQ 29 7 Gallery
More informationAgilent Genomic Workbench 7.0
Agilent Genomic Workbench 7.0 Workflow User Guide For Research Use Only. Not for use in diagnostic procedures. Agilent Technologies Notices Agilent Technologies, Inc. 2012, 2015 No part of this manual
More informationXStatic Documentation
XStatic Documentation Release 1.0.1 Thomas Waldmann Sep 18, 2018 Contents 1 What is XStatic 1 1.1 The Idea................................................. 1 1.2 Pros....................................................
More informationQTX. Tutorial for. by Kim M.Chmielewicz Kenneth F. Manly. Software for genetic mapping of Mendelian markers and quantitative trait loci.
Tutorial for QTX by Kim M.Chmielewicz Kenneth F. Manly Software for genetic mapping of Mendelian markers and quantitative trait loci. Available in versions for Mac OS and Microsoft Windows. revised for
More informationKEMP Driver for Red Hat OpenStack. KEMP LBaaS Red Hat OpenStack Driver. Installation Guide
KEMP LBaaS Red Hat OpenStack Driver Installation Guide VERSION: 2.0 UPDATED: AUGUST 2016 Copyright Notices Copyright 2002-2016 KEMP Technologies, Inc.. All rights reserved.. KEMP Technologies and the KEMP
More informationLight&Efficient&Flutter&Shutter&
LightEfficientFlutterShutter MosheBen)Ezra August2012 Abstract Flutter shutter is technique in which the exposure is chopped into segments and light is only integrated part of the time. By carefully selecting
More informationQuality of Service (QOS) With Tintri VM-Aware Storage
TECHNICAL WHITE PAPER Quality of Service (QOS) With Tintri VM-Aware Storage Dominic Cheah Technical Marketing Engineer (TME) Oct 2015 www.tintri.com Contents Intended Audience... 3 Consolidated List of
More informationProFont began life as a better version of Monaco 9 which is especially good for programmers. It was created circa 1987 by Andrew Welch.
Important Note This is the original readme file of the ProFont distribution for Apple Macintosh. If you re using ProFont on Windows or Unix, or downloaded any other ProFont package than»profont Distribution
More informationBluetooth Low Energy in C++ for nrfx Microcontrollers
Bluetooth Low Energy in C++ for nrfx Microcontrollers 1st Edition Tony Gaitatzis BackupBrain Publishing, 2017 ISBN: 978-1-7751280-7-6 backupbrain.co i Bluetooth Low Energy in C++ for nrfx Microcontrollers
More informationMoodle. Moodle. Deployment Guide
Moodle Deployment Guide VERSION: 6.0 UPDATED: MARCH 2016 Copyright Notices Copyright 2002-2016 KEMP Technologies, Inc.. All rights reserved.. KEMP Technologies and the KEMP Technologies logo are registered
More informationSimba Cassandra ODBC Driver with SQL Connector
Simba Cassandra ODBC Driver with SQL Connector Last Revised: March 26, 2013 Simba Technologies Inc. Copyright 2012-2013 Simba Technologies Inc. All Rights Reserved. Information in this document is subject
More informationJavaScript Libraries User's Guide
FUJITSU Software Interstage Application Server JavaScript Libraries User's Guide Windows/Solaris/Linux B1WS-1049-02ENZ0(00) November 2013 Preface Purpose of This Document This document provides information
More informationDocuments. OpenSim Tutorial. March 10, 2009 GCMAS Annual Meeting, Denver, CO. Jeff Reinbolt, Ajay Seth, Scott Delp. Website: SimTK.
Documents OpenSim Tutorial March 10, 2009 GCMAS Annual Meeting, Denver, CO Jeff Reinbolt, Ajay Seth, Scott Delp Website: SimTK.org/home/opensim OpenSim Tutorial Agenda 10:30am 10:40am Welcome and goals
More informationMigration Tool. Migration Tool (Beta) Technical Note
Migration Tool (Beta) Technical Note VERSION: 6.0 UPDATED: MARCH 2016 Copyright Notices Copyright 2002-2016 KEMP Technologies, Inc.. All rights reserved.. KEMP Technologies and the KEMP Technologies logo
More informationSW MAPS TEMPLATE BUILDER. User s Manual
SW MAPS TEMPLATE BUILDER User s Manual Copyright (c) 2017 SOFTWEL (P) Ltd All rights reserved. Redistribution and use in binary forms, without modification, are permitted provided that the following conditions
More informationXEP-0399: Client Key Support
XEP-0399: Client Key Support Dave Cridland mailto:dave.c@threadsstyling.com xmpp:dwd@dave.cridland.net 2018-01-25 Version 0.1.0 Status Type Short Name Experimental Standards Track client-key This specification
More informationXEP-0140: Shared Groups
XEP-0140: Shared Groups Peter Saint-Andre mailto:peter@andyetnet xmpp:stpeter@stpeterim https://stpeterim/ 2004-10-27 Version 02 Status Type Short Name Retracted Informational groups This document defines
More informationPiexif Documentation. Release 1.0.X. hmatoba
Piexif Documentation Release 1.0.X hmatoba Oct 06, 2017 Contents 1 About Piexif 3 1.1 What for?................................................. 3 1.2 How to Use................................................
More informationAdditional License Authorizations for HPE OneView for Microsoft Azure Log Analytics
Additional License Authorizations for HPE OneView for Microsoft Azure Log Analytics Product Use Authorizations This document provides Additional License Authorizations for HPE OneView for Microsoft Azure
More informationCS 4961 Senior Design. Planetary Surface Flyover Movie Generator. Software Design Specification
CS 4961 Senior Design Planetary Surface Flyover Software Design Specification Document Prepared by: Shawn Anderson Fidel Izquierdo Jr. Angel Jimenez Khang Lam Christopher Omlor Hieu Phan 02 December 2016
More informationPiexif Documentation. Release 1.0.X. hmatoba
Piexif Documentation Release 1.0.X hmatoba January 29, 2017 Contents 1 About Piexif 3 1.1 What for?................................................. 3 1.2 How to Use................................................
More information