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André F. Rendeiro afrendeiro

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@Mahedi-61
Mahedi-61 / cuda_11.8_installation_on_Ubuntu_22.04
Last active April 11, 2024 23:29
Instructions for CUDA v11.8 and cuDNN 8.9.7 installation on Ubuntu 22.04 for PyTorch 2.1.2
#!/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
@dfjenkins3
dfjenkins3 / IGV_Batch_Screenshots.md
Last active March 2, 2023 07:09
IGV Batch Screenshots

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
@karpathy
karpathy / min-char-rnn.py
Last active April 13, 2024 16:48
Minimal character-level language model with a Vanilla Recurrent Neural Network, in Python/numpy
"""
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)
@informationsea
informationsea / refFlat2Bed.py
Created June 28, 2015 11:21
Convert USCS refFlat.txt to BED format
#!/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'))
@dwyerk
dwyerk / concave_hulls.ipynb
Created April 12, 2014 23:20
concave hulls using shapely and scipy
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@keithshep
keithshep / querybiomartexample.py
Created December 3, 2013 20:05
A small example for how to create XML queries for biomart using python
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>''' \
@benbalter
benbalter / gist.md
Last active November 2, 2023 02:04
Example of how to embed a Gist on GitHub Pages using Jekyll.

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 %}.

@vgoklani
vgoklani / app.py
Last active December 19, 2022 09:13
Using Flask to output Python data to High Charts
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'}