mikelove

library(plyranges)

set.seed(1)
x <- data.frame(seqnames=1, start=0:9 * 100 + 1, 
                width=20, id=1:10) %>%
  as_granges()

y <- data.frame(seqnames=1, start=round(runif(4,100,900)), 
                width=10, id=letters[1:4]) %>%
  as_granges() %>%

willkurt

ilevantis

Bedtools Cheatsheet

General:

Tools	Description
flank	Create new intervals from the flanks of existing intervals.
slop	Adjust the size of intervals.
shift	Adjust the position of intervals.
subtract	Remove intervals based on overlaps b/w two files.

stefanthaler

"""
    Simple example to demostrate the embedding visualization for word embeddings in tensorflow / tensorboard
    https://www.tensorflow.org/how_tos/embedding_viz/
"""

import tensorflow as tf
import os
assert tf.__version__ == '1.0.0-rc0' # if code breaks, check tensorflow version
from tensorflow.contrib.tensorboard.plugins import projector

Brainiarc7

GNU Parallel for Bioinformatics: A primer

Installation:

A quick installation does not require root access, as shown:

(wget -O - pi.dk/3 || curl pi.dk/3/ || fetch -o - http://pi.dk/3) | bash

For other installation options see http://git.savannah.gnu.org/cgit/parallel.git/tree/README

stefanthaler

"""
Learning Task:
    Given a sequence, predict a label based on the first value of the sequence

Explanation of stateful LSTM and setup:
    http://philipperemy.github.io/keras-stateful-lstm/
    
Exmple:
    given a sequence [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], predict 1
    given a sequence [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], predict 0

bayesian_neural_network.ipynb

jfpuget

madjar

import asyncio
import aiohttp
import bs4
import tqdm


@asyncio.coroutine
def get(*args, **kwargs):
    response = yield from aiohttp.request('GET', *args, **kwargs)
    return (yield from response.read_and_close(decode=True))

sloria

The Best of the Best Practices (BOBP) Guide for Python

A "Best of the Best Practices" (BOBP) guide to developing in Python.

In General

Values

• "Build tools for others that you want to be built for you." - Kenneth Reitz
• "Simplicity is alway better than functionality." - Pieter Hintjens