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Leonardo Collado-Torres lcolladotor

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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
@lcolladotor
lcolladotor / WiggleTools-install-log
Created March 25, 2014 17:02
WiggleTools install log 2014-03-25
$ cd software/
12:47 software $ rm -fr userApps/
12:47 software $ git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git beta src/userApps > userApps.zip
12:47 software $ unzip -d userApps -j userApps.zip
Archive: userApps.zip
302e8a718e30b3025bceab6816841c8c72226291
inflating: userApps/GenomeBrowserLicense.pdf
inflating: userApps/Makefile
inflating: userApps/README
inflating: userApps/fetchKentSource.sh
@lcolladotor
lcolladotor / test.Rmd
Created April 10, 2014 22:45
test
=====
```{r}
plot(1:10)
```
@lcolladotor
lcolladotor / der2A-oVSy.run3-v0.0.46.chr1.e503632
Created April 23, 2014 19:08
Warning messages:
1: multiple methods tables found for ‘mold’
2: In fun(libname, pkgname) : no DISPLAY variable so Tk is not available
Loading Rdata file with the output from loadCoverage()
2014-04-17 15:59:06 analyzeChr: Pre-processing the coverage data
2014-04-17 15:59:06 preprocessCoverage: using chunksize 3952762
2014-04-17 16:09:20 preprocessCoverage: splitting the data
2014-04-17 16:14:51 analyzeChr: Calculating statistics
2014-04-17 16:14:51 calculateStats: calculating the F-statistics
2014-04-17 16:21:26 analyzeChr: Calculating pvalues
@lcolladotor
lcolladotor / der2R-oVSy.run2-v0.0.46.e659794
Created April 23, 2014 20:08
Warning message:
In fun(libname, pkgname) : no DISPLAY variable so Tk is not available
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
@lcolladotor
lcolladotor / .Rprofile
Created June 5, 2014 20:34
Cluster R profile
## Fix libpath for R 3.1.x
if(commandArgs()[1] == "/jhpce/shared/community/compiler/gcc/4.4.7/R/3.1.x/lib64/R/bin/exec/R") {
dir.create("~/R/x86_64-unknown-linux-gnu-library/3.1.x", showWarnings=FALSE, recursive=TRUE)
message("Using the following user library: ~/R/x86_64-unknown-linux-gnu-library/3.1.x")
.libPaths(c("~/R/x86_64-unknown-linux-gnu-library/3.1.x", "/jhpce/shared/community/compiler/gcc/4.4.7/R/3.1.x/lib64/R/site-library", "/jhpce/shared/community/compiler/gcc/4.4.7/R/3.1.x/lib64/R/library"))
}