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Nacho Caballero nachocab

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nachocab / gist:4931cc20084472941e85
Created April 29, 2015 16:02
targets <- read.table("targets.txt", header = TRUE)
counts <- read.delim("counts.txt", row.names = "gene_id")
counts <- counts[, targets$sample_name] # important, the ordering of the columns in the counts file must match the sample_name in the targets file
group <- factor(targets$virus_dpi, levels = unique(targets$virus_dpi))
library(edgeR)
y <- DGEList(counts = counts, group = group)
y <- calcNormFactors(y)
design <- model.matrix( ~ 0 + group, data = y$samples)
@nachocab
nachocab / mds.jpg
Last active December 18, 2015 08:46
mds.jpg
@nachocab
nachocab / to_bam_pbmc_08_12.log
Created November 19, 2014 15:31
Sender: LSF System <lsf@node1667>
Subject: Job 2941808: <to_bam_pbmc_08_12> Exited
Job <to_bam_pbmc_08_12> was submitted from host <tin> by user <icaballe> in cluster <cromwell>.
Job was executed on host(s) <node1667>, in queue <hour>, as user <icaballe> in cluster <cromwell>.
</home/unix/icaballe> was used as the home directory.
</idi/sabeti-data/nacho/ebola_pbmc2> was used as the working directory.
Started at Tue Nov 18 20:00:26 2014
Results reported at Tue Nov 18 21:48:17 2014
@nachocab
nachocab / _.md
Last active August 29, 2015 14:09
sin waves
@nachocab
nachocab / index.html
Created November 11, 2014 01:05
criss cross
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<base target="_blank"> <!-- open all links on a new tab -->
<!-- <script src="bower_components/d3/d3.js"></script> -->
<script src="http://d3js.org/d3.v3.min.js"></script>
<style>
body{
@nachocab
nachocab / index.html
Created November 11, 2014 01:05
criss cross
an
@nachocab
nachocab / criss_cross_pattern.html
Created November 11, 2014 01:03
criss cross
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<base target="_blank"> <!-- open all links on a new tab -->
<!-- <script src="bower_components/d3/d3.js"></script> -->
<script src="http://d3js.org/d3.v3.min.js"></script>
<style>
body{
@nachocab
nachocab / criss_cross_pattern.html
Created November 11, 2014 01:01
criss cross pattern
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<base target="_blank"> <!-- open all links on a new tab -->
<script src="bower_components/d3/d3.js"></script>
<style>
body{
font-size: 20px;
@nachocab
nachocab / gist:7913087
Created December 11, 2013 16:04
data <- structure(list(gene = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L,
8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L,
21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L,
34L, 35L, 36L, 37L, 38L, 39L, 40L, 1L, 2L, 3L, 4L, 5L, 6L, 7L,
8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L,
21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L,
34L, 35L, 36L, 37L, 38L, 39L, 40L, 1L, 2L, 3L, 4L, 5L, 6L, 7L,
8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L,
21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L,
34L, 35L, 36L, 37L, 38L, 39L, 40L, 1L, 2L, 3L, 4L, 5L, 6L, 7L,
@nachocab
nachocab / gist:7272792
Created November 1, 2013 22:10
$ ssh -vvv nacho@scc4.bu.edu 11/01/2013 18:59:25 GFT
OpenSSH_6.2p2, OSSLShim 0.9.8r 8 Dec 2011
debug1: Reading configuration data /Users/nacho/.ssh/config
debug1: /Users/nacho/.ssh/config line 1: Applying options for *
debug1: Reading configuration data /etc/ssh_config
debug1: /etc/ssh_config line 20: Applying options for *
debug1: /etc/ssh_config line 53: Applying options for *
debug2: ssh_connect: needpriv 0
debug1: Connecting to scc4.bu.edu [10.48.225.54] port 22.
debug1: Connection established.