nachocab

calstad

Quick List of Resources for Topological Data Analysis with Emphasis on Machine Learning

This is just a quick list of resourses on TDA that I put together for @rickasaurus after he was asking for links to papers, books, etc on Twitter and is by no means an exhaustive list.

Survey Papers

Both Carlsson's and Ghrist's survey papers offer a very good introduction to the subject

• Topology and Data by Gunnar Carlsson
• Barcodes: The Persistent Topology of Data by Robert Ghrist

Other Papers and Web Resources

• Extracting insights from the shape of complex data using topology A good introductory paper in Nature on the Mapper algorithm.

yannabraham

library(Biobase)
library(flowCore)
library(flowViz)

# simply replace the dummy dta below with your CSV data
dta <- matrix(rnorm(10000),ncol=10)
dimnames(dta)[[2]] <- LETTERS[1:10]

head(dta)

stvhwrd

###While this script does concatenate pdf files, I haven't yet figured out in which order it does so. On a sample of 19 pdf files, logically named 01something.pdf, 02something.pdf, 03something.pdf, etc. the order of the merged product seemed almost random...

...from Tiger onwards, OSX ships with a Python script that concatenates pdf files (merges them together). The script is already executable, and Python is pre-installed on OS X, so all you need to do is point it at your pdf files and run

"/System/Library/Automator/Combine PDF Pages.action/Contents/Resources/join.py" -o PATH/TO/YOUR/MERGED/FILE.pdf /PATH/TO/ORIGINAL/1.pdf /PATH/TO/ANOTHER/2.pdf /PATH/TO/A/WHOLE/DIR/*.pdf

I prefer putting the link in /usr/local/bin, as it is in the $PATH and therefore I can run the command from anywhere. To set up the link, you need to navigate to the directory where you want the link.

azam

convert -density 256x256 -background transparent favicon.svg -define icon:auto-resize -colors 256 favicon.ico

hlissner

# ag <https://github.com/ggreer/the_silver_searcher>
# usage: ag-replace.sh [search] [replace]
# caveats: will choke if either arguments contain a forward slash
# notes: will back up changed files to *.bak files

ag -0 -l $1 | xargs -0 perl -pi.bak -e "s/$1/$2/g"

# or if you prefer sed's regex syntax:

ag -0 -l $1 | xargs -0 sed -ri.bak -e "s/$1/$2/g"

nimishzynga

tell application "System Events"
	-- get current clipboard contents as a string
	set CurrentClipboard to the clipboard as string
	
	-- set the clipboad to your password	
	set the clipboard to "Y0urVPNPa$$w0rd"
	
	-- start playing with the VPN	
	tell current location of network preferences
		

msund

{
 "metadata": {
  "name": "",
  "signature": "sha256:4abc3bda22c03a05e4c028a06c0fdb0efbd5a6220ac512d85f9529fe8f08d9b7"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [

lindenb

REF=/path/to/ref.fasta
.PHONY:all

all: align/variants.vcf

align/variants.vcf:  align/Sample1_sorted.bam  align/Sample2_sorted.bam  align/Sample3_sorted.bam 
	/path/to/samtools mpileup -uf ${REF}  $^  |\
	/path/to/bcftools view -vcg - >$@

msund

{
 "metadata": {
  "name": "Reproducible figures"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {