karpathy

"""
Minimal character-level Vanilla RNN model. Written by Andrej Karpathy (@karpathy)
BSD License
"""
import numpy as np

# data I/O
data = open('input.txt', 'r').read() # should be simple plain text file
chars = list(set(data))
data_size, vocab_size = len(data), len(chars)

Mahedi-61

#!/bin/bash

### steps ####
# Verify the system has a cuda-capable gpu
# Download and install the nvidia cuda toolkit and cudnn
# Setup environmental variables
# Verify the installation
###

### to verify your gpu is cuda enable check

benbalter

Here's an example of how to embed a Gist on GitHub Pages:

{% gist 5555251 %}

All you need to do is copy and paste the Gist's ID from the URL (here 5555251), and add it to a gist tag surrounded by {% and %}.

dwyerk

dfjenkins3

IGV Batch Screenshots

IGV provides functionality that allows a user to create a script to take screenshots of regions of interest.

Table of Contents

1. Requirements
2. Workflow
3. Create BED File

vgoklani

from flask import Flask, render_template

app = Flask(__name__)

@app.route('/')
@app.route('/index')
def index(chartID = 'chart_ID', chart_type = 'bar', chart_height = 350):
	chart = {"renderTo": chartID, "type": chart_type, "height": chart_height,}
	series = [{"name": 'Label1', "data": [1,2,3]}, {"name": 'Label2', "data": [4, 5, 6]}]
	title = {"text": 'My Title'}

informationsea

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import argparse
import csv

def _main():
    parser = argparse.ArgumentParser(description="Convert RefFlat to BED format")
    parser.add_argument('refFlat', type=argparse.FileType('r'))
    parser.add_argument('outputBed', type=argparse.FileType('w'))

keithshep

import requests

def main():
    exampleTaxonomy = "mmusculus_gene_ensembl"
    exampleGene = "ENSMUSG00000086981"

    urlTemplate = \
        '''http://ensembl.org/biomart/martservice?query=''' \
        '''<?xml version="1.0" encoding="UTF-8"?>''' \
        '''<!DOCTYPE Query>''' \