pmav99

{
  "logging": {
    "version": 1,
    "disable_existing_loggers": true,
    "formatters": {
      "brief": {
        "class": "logging.Formatter",
        "datefmt": "%I:%M:%S",
        "format": "%(levelname)-8s; %(name)-15s; %(message)s"
      },

crazyhottommy

#! /usr/bin/env python

# ID mapping using mygene
# https://pypi.python.org/pypi/mygene
# http://nbviewer.ipython.org/gist/newgene/6771106
# http://mygene-py.readthedocs.org/en/latest/
# 08/30/14

__author__ = 'tommy'

bsweger

Useful Pandas Snippets

A personal diary of DataFrame munging over the years.

Data Types and Conversion

Convert Series datatype to numeric (will error if column has non-numeric values)
(h/t @makmanalp)

jdblischak

Differential expression analysis with edgeR

This is a tutorial I have presented for the class Genomics and Systems Biology at the University of Chicago. In this course the students learn about study design, normalization, and statistical testing for genomic studies. This is meant to introduce them to how these ideas are implemented in practice. The specific example is a differential expression analysis with edgeR starting with a table of counts and ending with a list of differentially expressed genes.

Past versions:

• Tuesday, April 26, 2016

trestletech

library(shiny)
library(ggplot2)

# Get the current day of the month
dom <- 25

# Define the target for salespeople in our organization.
salesTarget <- 15000

# Set the seed so we always get the same data.

rxaviers

People

:bowtie:	😄 :smile:	😆 :laughing:
😊 :blush:	😃 :smiley:	☺️ :relaxed:
😏 :smirk:	😍 :heart_eyes:	😘 :kissing_heart:
😚 :kissing_closed_eyes:	😳 :flushed:	😌 :relieved:
😆 :satisfied:	😁 :grin:	😉 :wink:
😜 :stuck_out_tongue_winking_eye:	😝 :stuck_out_tongue_closed_eyes:	😀 :grinning:
😗 :kissing:	😙 :kissing_smiling_eyes:	😛 :stuck_out_tongue:

astrofrog

import os
import random
import string
import tempfile
import subprocess

def random_id(length=8):
    return ''.join(random.sample(string.ascii_letters + string.digits, length))

TEMPLATE_SERIAL = """

sidderb

library(shiny)
library(deSolve)
library(cummeRbund)

# load cuffDiff data, must be in top dir and called cuffData.db:
cuff = readCufflinks()

shinyServer(function(input,output) {
    
	getData = reactive(function() {

mgalardini

#!/usr/bin/python
'''
Launch codeml on all the alignments

Marco Galardini 2012
University of Florence
GPL v3.0
'''
from optparse import OptionParser, OptionGroup
from time import strftime

hoffrocket

#!/usr/bin/env python

from multiprocessing import Process, Pool
import time
import urllib2

def millis():
  return int(round(time.time() * 1000))

def http_get(url):