Skip to content

Instantly share code, notes, and snippets.

View nachocab's full-sized avatar

Nacho Caballero nachocab

110 followers · 24 following
View GitHub Profile
@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.
@nachocab
nachocab / awk_for_kate
Created September 18, 2013 18:01
# Create a file with the awk code
echo '
$6 == "protein_coding" {
gene_counter[$10] += 1
}
END {
for (gene_name in gene_counter){
print gene_name, gene_counter[gene_name]
}
@nachocab
nachocab / html.r
Created June 14, 2013 20:32 — forked from hadley/html.r
# We first start by creating a way of escaping the characters that have special
# meaning for html, while making sure we don't end up double-escaping at any
# point. The easiest way to do this is to create an S3 class that allows us to
# distinguish between regular text (that needs escaping) and html (that
# doesn't).
#
# We then write an escape method that leaves html unchanged and escapes the
# special characters (&, <, >) in ordinary text. We also add a method for lists
# for convenience
@nachocab
nachocab / mds.jpg
Last active December 18, 2015 08:46
mds.jpg
@nachocab
nachocab / index.html
Created May 29, 2013 11:49 — forked from rduplain/responsive_d3_example.html
<!DOCTYPE html>
<script src="http://mbostock.github.com/d3/d3.v2.js?2.8.1"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script>
<style>
body {
font: 10px sans-serif;
}
rect {
@nachocab
nachocab / sequencing.sh
Created May 24, 2013 20:32
Commands used to count reads in the filone and yang_a datasets.
tophat --version
# Tophat v2.0.0
# filone
for LANE in 0 0_5 2 6 18; do
tophat --library-type fr-unstranded \
--solexa1.3-quals \
--segment-length 18 \
--no-coverage-search \
--no-novel-juncs \
@nachocab
nachocab / _.md
Created May 19, 2013 16:33
Tributary inlet
@nachocab
nachocab / _.md
Created May 19, 2013 13:04
crossfilter racetrack
@nachocab
nachocab / _.md
Created May 19, 2013 12:52
Tributary inlet