IBG Wiki - keller_and_evans_lab

cu_research_computing

anonymous@undisclosed.example.com (Anonymous) — Wed, 12 Feb 2020 16:03:05 +0000

This document will mostly cover specific instructions for using RC in the Vrieze and Keller labs. We will try to update this, but RC is a bit of a moving target, so some of what is written below may now be outdated. Getting started General documentation for using RC is

dev_con

anonymous@undisclosed.example.com (Anonymous) — Thu, 31 Oct 2019 16:48:23 +0000

Slides and notes from meetings 16_cadd_mls Descriptives Colorado Community Twin Study (CTS) and Longitudinal Twin Study (LTS) Descriptives Wave Sample Size - SAM % Male Mean (SD) Age Mean (SD) CPD CTS Wave 1 2005 47% 15.95 (1.73) NA CTS Wave 2 1743 45%

fall_2016_goals

anonymous@undisclosed.example.com (Anonymous) — Thu, 31 Oct 2019 16:47:51 +0000

Rasool - * Finish IQ ~ GxSES submit by December * submit Mathematical Bio NSF grant in November * Figure out if we want to try to do another GeneEvolve MS or work on shared hapltoype stuffs Luke - * submit K01 in October * have snp-h2 comparison method paper to HRC by end of November

fall_2016_schedule

anonymous@undisclosed.example.com (Anonymous) — Thu, 31 Oct 2019 16:47:51 +0000

Please sign up below (one person per lab meeting) for speaking at lab meetings this semester. Please prepare slides and please take a few slides to introduce background to the problem so that other people in the lab understand what you're doing and can contribute to the conversation.

gscan_db_ga_p

anonymous@undisclosed.example.com (Anonymous) — Thu, 31 Oct 2019 18:28:12 +0000

UK Biobank More information about the files used for UKBiobank are here. In brief, we used the UK10K + 1kgp3 imputed vcfs provided by UKBionank and added in dosages w/ this python script: import gzip, argparse, re, os, datetime from subprocess import Popen, PIPE def add_dosage(pair):

gscan

anonymous@undisclosed.example.com (Anonymous) — Mon, 28 Oct 2019 21:59:50 +0000

GSCAN--or the GWAS & Sequencing Consortium of Alcohol and Nicotine use--is an international genetic association meta-analysis consortium. Our goal is to aggregate genetic association findings across scores of studies with millions of individuals. GSCAN is composed of three independent but related projects: 1) an exome chip meta-analysis of low-frequency non-synonymous variants, 2) a GWAS meta-analysis, and 3) a whole genome sequencing association meta-analysis.

lab_meeting

anonymous@undisclosed.example.com (Anonymous) — Fri, 21 Feb 2025 18:12:49 +0000

Spring 2022 - All Lab Meetings Please sign up below to present at the statistical genetics group meetings. Note that Joint lab meetings are biweekly, and that lab meetings with CU Anschutz are first Wed of each month. Date Lab meeting Presenter January 05

meeting_notes

anonymous@undisclosed.example.com (Anonymous) — Thu, 31 Oct 2019 16:50:27 +0000

notes for 9/6/17

members

anonymous@undisclosed.example.com (Anonymous) — Tue, 17 Dec 2019 22:14:52 +0000

Page in progress...

my_sql

anonymous@undisclosed.example.com (Anonymous) — Thu, 31 Oct 2019 16:50:27 +0000

MySQL Connecting to MySQL server in bash # Connect to mysql server mysql --host= --user= --password= MySQL commands show databases; # show the databases use userdata_schema; # connect to a particular database show tables; # list the tables within the database select * from table_name limit 10; # to see what's in a table (first ten entries) select * from user_location where user_id='6346669087044735461' order by sample_time desc limit 10;

regular_expressions

anonymous@undisclosed.example.com (Anonymous) — Thu, 31 Oct 2019 16:50:27 +0000

Testing regular expression (in javascript or python)

spring_2017_goals

anonymous@undisclosed.example.com (Anonymous) — Thu, 31 Oct 2019 16:50:26 +0000

David - * Submit GSCAN exome paper * have submitted manuscript of initial co-twins paper * Completing QC on parental monitoring and substance use data * Completing QC on location data * Concordance analysis between Michigan and Colorado / trajectory

start

anonymous@undisclosed.example.com (Anonymous) — Wed, 05 May 2021 17:27:52 +0000

Welcome to the [[http://www.colorado.edu/ibg|IBG]] Statistical Genetics Group Wiki! This wiki is maintained by the Statistical Genetics research labs of at IBG - Keller, Evans, Friedman, Ehringer, Grotzinger, and others. We are a research group at the

uk_biobank

anonymous@undisclosed.example.com (Anonymous) — Thu, 31 Oct 2019 16:50:26 +0000

How the data was prepared * downloading_the_data Using the UK Biobank data * file_locations Phenotype information * phenotypes Requests for additional phenotypes * phenotype_request projects meeting_notes

unix_basics

anonymous@undisclosed.example.com (Anonymous) — Tue, 29 Oct 2019 00:20:57 +0000

Basics moves or renames files mv file destination copies files cp file destination lists files in directory ls ls -ltrah look at what processes are running on server (for CPU and RAM usage)