yannabraham’s gists

miquelrojascherto / gist:151205

Created July 21, 2009 08:37

	//Demonstrates basic manipulation to predict a EI-MS in Bioclipse using
	//a sdf file containing a list of molecule.
	//Requires medea data installed in default location
	var mols = cdk.loadMolecules("/Sample Data/SDFfiles/CAS.5.sdf");
	for (var i = 0; i < mols.size(); i++) {
	var mol = mols.get(i);
	mol = cdk.generate2dCoordinates(mol);
	ui.open(mol);

	cmlSpectrum = medea.predictMassSpectrum(mol)

mattismyname / imgupload.py

Created January 3, 2011 04:20

Python script to upload a batch of files to Evernote

	#!/usr/bin/env python
	#
	# To run, first set this environment variable to point to the Evernote API python bindings you downloaded from Evernote:
	# export PYTHONPATH=/path/to/evernote/python/api
	#

	import sys
	import hashlib
	import time
	import thrift.protocol.TBinaryProtocol as TBinaryProtocol

drewconway / noticeEMail.py

Created April 12, 2011 20:42

Sends an email message through GMail once the script is completed. Developed to be used with AWS (or other system) so that instances can be terminated once a long job is done. Only works for those with GMail accounts.

	#!/usr/bin/env python
	# encoding: utf-8

	import smtplib
	from datetime import datetime


	def noticeEMail(starttime, usr, psw, fromaddr, toaddr):
	"""
	Sends an email message through GMail once the script is completed.

lindenb / translate.html

Created April 22, 2011 20:29

Translate a DNA to protein using HTML5+ File API.

	<html>
	<head>

	</head>
	<body>
	<form>
	<label for="ZmlsZXMKfiles">Select a FASTA file</label>:<input type="file" id="ZmlsZXMKfiles" multiple="true"/>
	</form>
	<script type="application/ecmascript">

mbostock / .block

Last active February 26, 2019 22:38

Horizon Chart

	license: gpl-3.0
	redirect: https://observablehq.com/@d3/d3-horizon-chart

simecek / facebook_friendship1.r

Created January 18, 2012 11:28

Facebook Friendship Graph

	# the code uses 'facebook' function from the previous gist (https://gist.github.com/1634662) or
	# see the original http://romainfrancois.blog.free.fr/index.php?post/2012/01/15/Crawling-facebook-with-R

	# scrape the list of friends
	friends <- facebook( path="me/friends" , access_token=access_token)
	# extract Facebook IDs
	friends.id <- sapply(friends$data, function(x) x$id)
	# extract names
	friends.name <- sapply(friends$data, function(x) iconv(x$name,"UTF-8","ASCII//TRANSLIT"))
	# short names to initials

jeromyanglim / example-r-markdown.rmd

Created May 17, 2012 04:23

Example of using R Markdown

	This post examines the features of [R Markdown](http://www.rstudio.org/docs/authoring/using_markdown)
	using [knitr](http://yihui.name/knitr/) in Rstudio 0.96.
	This combination of tools provides an exciting improvement in usability for
	[reproducible analysis](http://stats.stackexchange.com/a/15006/183).
	Specifically, this post
	(1) discusses getting started with R Markdown and `knitr` in Rstudio 0.96;
	(2) provides a basic example of producing console output and plots using R Markdown;
	(3) highlights several code chunk options such as caching and controlling how input and output is displayed;
	(4) demonstrates use of standard Markdown notation as well as the extended features of formulas and tables; and
	(5) discusses the implications of R Markdown.

bobthecat / Rcpp_cosine.r

Created June 9, 2012 23:29

Rcpp cosine similarity

	require(inline)
	require(RcppArmadillo)

	## extract cosine similarity between columns
	cosine <- function(x) {
	y <- t(x) %*% x
	res <- 1 - y / (sqrt(diag(y)) %*% t(sqrt(diag(y))))
	return(res)
	}

dsparks / stat_2d.R

Created November 13, 2012 02:06

Encoding two-dimensional density in graphical variables

	doInstall <- TRUE # Change to FALSE if you don't want packages installed.
	toInstall <- c("ggplot2")
	if(doInstall){install.packages(toInstall, repos = "http://cran.r-project.org")}
	lapply(toInstall, library, character.only = TRUE)

	# Generate some randomly-distributed data
	nObs <- 5000
	myData <- data.frame(X = rnorm(nObs), Y = rnorm(nObs))
	nClusters <- 7 # Cluster it
	kMeans <- kmeans(myData, centers = nClusters)

cengel / server.R

Created November 15, 2012 00:44

Shiny intro tutorial example rewritten for ggplot2

	library(shiny)
	library(datasets)
	library(ggplot2) # load ggplot

	# Define server logic required to plot various variables against mpg
	shinyServer(function(input, output) {

	# Compute the forumla text in a reactive function since it is
	# shared by the output$caption and output$mpgPlot functions
	formulaText <- reactive(function() {

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