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Leonardo Collado-Torres lcolladotor

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lcolladotor / info.plist
Created February 18, 2014 19:17
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>contactEmailRot13</key>
<string>chris.fonnesbeck@vanderbilt.edu</string>
<key>contactName</key>
<string>Chris Fonnesbeck</string>
<key>description</key>
<string>Dynamic report generation in R</string>
@lcolladotor
lcolladotor / knit to html.tmCommand
Created February 18, 2014 19:38
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>beforeRunningCommand</key>
<string>saveActiveFile</string>
<key>command</key>
<string>#!/usr/bin/env bash
[[ -f "${TM_SUPPORT_PATH}/lib/bash_init.sh" ]] &amp;&amp; . "${TM_SUPPORT_PATH}/lib/bash_init.sh"
@lcolladotor
lcolladotor / Rmarkdown test.Rmd
Created February 20, 2014 03:12
R Markdown test
===============
# Title 1
## Title 2
### Title 3
#### Title 4
Headings work.
@lcolladotor
lcolladotor / index.html
Created February 26, 2014 02:22
test publish
<!doctype HTML>
<meta charset = 'utf-8'>
<html>
<head>
<script src='http://d3js.org/d3.v3.min.js' type='text/javascript'></script>
<script src='http://d3js.org/topojson.v1.min.js' type='text/javascript'></script>
<script src='http://datamaps.github.io/scripts/datamaps.all.min.js' type='text/javascript'></script>
<script src='http://cdnjs.cloudflare.com/ajax/libs/handlebars.js/1.0.0/handlebars.min.js' type='text/javascript'></script>
<script src='http://cdnjs.cloudflare.com/ajax/libs/angular.js/1.2.1/angular.min.js' type='text/javascript'></script>
@lcolladotor
lcolladotor / index.html
Created February 26, 2014 02:24
test publish 2
<!doctype HTML>
<meta charset = 'utf-8'>
<html>
<head>
<script src='http://d3js.org/d3.v3.min.js' type='text/javascript'></script>
<script src='http://d3js.org/topojson.v1.min.js' type='text/javascript'></script>
<script src='http://datamaps.github.io/scripts/datamaps.all.min.js' type='text/javascript'></script>
<script src='http://cdnjs.cloudflare.com/ajax/libs/handlebars.js/1.0.0/handlebars.min.js' type='text/javascript'></script>
<script src='http://cdnjs.cloudflare.com/ajax/libs/angular.js/1.2.1/angular.min.js' type='text/javascript'></script>
@lcolladotor
lcolladotor / index.html
Last active August 29, 2015 13:56
test publish 4
<!doctype HTML>
<meta charset = 'utf-8'>
<html>
<head>
<script src='http://d3js.org/d3.v3.min.js' type='text/javascript'></script>
<script src='http://d3js.org/topojson.v1.min.js' type='text/javascript'></script>
<script src='http://datamaps.github.io/scripts/datamaps.all.min.js' type='text/javascript'></script>
<script src='http://cdnjs.cloudflare.com/ajax/libs/handlebars.js/1.0.0/handlebars.min.js' type='text/javascript'></script>
<script src='http://cdnjs.cloudflare.com/ajax/libs/angular.js/1.2.1/angular.min.js' type='text/javascript'></script>
@lcolladotor
lcolladotor / index.html
Created February 26, 2014 03:02
test publish 4
<!doctype HTML>
<meta charset = 'utf-8'>
<html>
<head>
<script src='http://d3js.org/d3.v3.min.js' type='text/javascript'></script>
<script src='http://d3js.org/topojson.v1.min.js' type='text/javascript'></script>
<script src='http://datamaps.github.io/scripts/datamaps.all.min.js' type='text/javascript'></script>
<script src='http://cdnjs.cloudflare.com/ajax/libs/handlebars.js/1.0.0/handlebars.min.js' type='text/javascript'></script>
<script src='http://cdnjs.cloudflare.com/ajax/libs/angular.js/1.2.1/angular.min.js' type='text/javascript'></script>
@lcolladotor
lcolladotor / index.html
Created February 26, 2014 04:26
Intentional homicides rates for Mexico 1997-2013
<!doctype HTML>
<meta charset = 'utf-8'>
<html>
<head>
<script src='http://d3js.org/d3.v3.min.js' type='text/javascript'></script>
<script src='http://d3js.org/topojson.v1.min.js' type='text/javascript'></script>
<script src='http://datamaps.github.io/scripts/datamaps.all.min.js' type='text/javascript'></script>
<script src='http://cdnjs.cloudflare.com/ajax/libs/handlebars.js/1.0.0/handlebars.min.js' type='text/javascript'></script>
<script src='http://cdnjs.cloudflare.com/ajax/libs/angular.js/1.2.1/angular.min.js' type='text/javascript'></script>
@lcolladotor
lcolladotor / rnaseq.md
Last active August 29, 2015 13:57 — forked from alyssafrazee/rnaseq.md

Title: Analyzing RNA-seq data with the "Tuxedo" tools Date: 2014-03-04 22:30 Slug: rnaseq

Introduction/tl;dr: I wrote this post as a reference for a few new graduate students in my department that are getting started with RNA-seq data analysis. It begins with an informal, big-picture overview of RNA-seq data analysis, and the general flow of the post outlines one standard RNA-seq workflow, but I wanted to give general audiences a "heads-up" that the post goes into quite a bit of nitty gritty detail that's specific to our department's computing setup.

preliminaries: what's RNA-seq?

RNA-seq is a high-throughput technology used to measure gene expression in cell populations. For a super bare-bones picture of what gene expression is, please enjoy this ASCII art I made to illustrate the process:

@lcolladotor
lcolladotor / install-log.txt
Last active August 29, 2015 13:57
Wigtools install log
21:38 ~ $ cd software/
21:38 software $ ls
aspera-connect-2.7.9.58060-linux-64.sh HTSeq-0.5.4p5 localpython mercurial-2.3 Python-2.7.6rc1 rmate ruby-2.0.0-p353 sratoolkit.2.1.16-centos_linux64
cufflinks2_rc.Linux_x86_64 HTSeq-0.5.4p5.tar localruby numpy Python-2.7.6rc1.tgz Rtmp ruby-2.0.0-p353.tar.gz
21:38 software $
21:38 software $
21:38 software $ git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git beta src/userApps > userApps.zip
21:38 software $ unzip -d userApps -j userApps.zip
Archive: userApps.zip
302e8a718e30b3025bceab6816841c8c72226291