R. Burke Squires

Login: burkesquires

Company: NIAID BCBB

Location: Maryland

Bio: Catholic husband and father! DJM! Computational Biologist, Python guru, training "Dean", software "Czar" at NIAID / NIH. Computer science Ph.D. Candidate at...

Blog: www.burkesquires.com

Blog: www.burkesquires.com

Member of

1. Reproducible Science Curriculum

Repositories

2005-10-01-nih

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2015-tutorials

tutorials for 2015 EDAMAME

2016-tutorials

repo for 2016 EDAMAME tutorials

2017-03-15-duke

Reproducible Research with the Jupyter notebook workshop at Duke

academic-kickstart

Easily create a beautiful website using Academic and Hugo

academicpages.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

advent_of_code_2017

Advent of Code 2017

AI-auto-managing-directory

This is a sample script of my simple AI projects. This script will managing your files (ex: grouping files on same kind) in your computer directory.

AlgoWiki

:globe_with_meridians: Repository which contains links and resources on different topics of Computer Science

angus

Materials for Analyzing Next-Generation Sequencing (ANGUS) course.

ARF-Converter

Bulk ARF file converter

augur

Pipeline components for real-time virus analysis

automation-RR-Jupyter

Automation with Jupyter notebooks

autotagger

Tag .mp3 and .m4a audio files from iTunes data automatically.

awesome-deepbio

A curated list of awesome deep learning applications in the field of computational biology

awesome-deep-learning-papers

The most cited deep learning papers

awesome-learn-to-programm-in-python

Python Programming Resources (especially for scientists, even more so for biologists)

awesome-machine-learning-python

Machine and Deep Learning in Python

awesome-reproducible-research

A collection of awesome resources related to reproducible research and open science

bc

Template for Software Carpentry bootcamp site repository.

becoming_a_reproducible_scientist

Becoming a reproducible scientist (a minimal tutorial)

BIOF309-2016-Fall

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BIOF509

Machine Learning and Object Oriented Programming with Python

bioinformatics-notes

Lecture notes for teaching biologists the basics of Linux/Unix and bioinformatics tools

bioinf-python

Python for Bioinformatics

biopython-notebook

Introduction to BioPython with iPython Notebooks

blocks

A Theano framework for building and training neural networks

bokeh-notebooks

Interactive Web Plotting with Bokeh in IPython notebook

Build-a-Reproducible-Jupyter-Workflow-From-Scratch

2017 NIH Hour of Code

Build-a-Reproducible-Jupyter-Workflow-From-Scratch

2017 NIH Hour of Code

Buku

Highly delicious bookmark manager. Your mini web!

char-rnn-tensorflow

Multi-layer Recurrent Neural Networks (LSTM, RNN) for character-level language models in Python using Tensorflow

Command_Line_for_Biologists

Introduction to Command Line for Biologists

computational-project-cookie-cutter

A cookie cutter to set up a folder structure for a computational project

cookbook-code

Recipes of the IPython Cookbook, the definitive guide to high-performance scientific computing and data science in Python

cookiecutter

A command-line utility that creates projects from cookiecutters (project templates). E.g. Python package projects, jQuery plugin projects.

cookiecutter-data-science

A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.

cookiecutter-reproducible-science

boilerplate for reproducible and transparent science

crestify

Intelligent Bookmarking

cytometry-clustering-comparison

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

DanQ

A hybrid convolutional and recurrent neural network for predicting the function of DNA sequences

data-exploration-RR-Jupyter

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data-journalism

Data journalism and easy to replicate notebooks using Python, R, and Web visualisations

datasharing

The Leek group guide to data sharing

deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine

DE_network_visualizer

tool for exploratory network analysis of differential expression data

dirsort

Automatic media file classification

dl-rnn

Recurrent Deep Learning Tutorials and examples: RNN, GRU, LSTM

document_cluster

A guide to document clustering in Python

dragonn

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

example-code

Example code for the book Fluent Python

eyeD3

eyeD3 is a Python module and command line program for processing ID3 tags. Information about mp3 files (i.e bit rate, sample frequency, play time, etc.) is also provided. The formats supported are ID3v1 (1.0/1.1) and ID3v2 (2.3/2.4).

FlowCytometryScripts

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FlowCytometryTools

A python package for visualization and analysis of high-throughput flow cytometry data

flusim

Influenza Molecular Infection Model & Discrete-Event Simulation

flusim-simjava

Influenza molecular infection and discrete event stochastic simulation based upon the simjava library

freeCodeCamp

The https://freeCodeCamp.com open source codebase and curriculum. Learn to code and help nonprofits.

genomics

Scripts, utilities and programs for genomic bioinformatics.

git-novice

Software Carpentry introduction to Git for novices.

git-test

A git test repository

Git-Tutorial

A basic git tutorial for my lab.

goatools

Python scripts to find enrichment of GO terms

handson-ml

A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in python using Scikit-Learn and TensorFlow.

homebrew-bioinformatics-linux

:beer: :penguin: Homebrew formulae for bioinformatics software only available for Linux

hour_of_code_python

NIH Hour of Code - Python Programming

hugo-academic

The website designer for Hugo. Build and deploy a beautiful website in minutes :rocket:

immunology-informatics

Immunology Informatics - Big Data Analysis in Immunology - Tutorials

influenza-ontology

Automatically exported from code.google.com/p/influenza-ontology

intro-ipython-notebook

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intro_programming

A set of IPython notebooks and learning resources for an Introduction to Programming class, focusing on Python.

iOS_ML

List of Machine Learning, AI, NLP solutions for iOS. The most recent version of this article can be found on my blog.

isp-data-pollution

ISP Data Pollution to Protect Private Browsing History with Obfuscation

jupyter-pathway

Canonical pathway visualization and analysis

keras

Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano or TensorFlow.

keras-flask-deploy-webapp

:smiley_cat: Pretty&simple image classifier app template. Deploy your own trained model or pre-trained model (VGG, ResNet, Densenet) to a web app using Flask in 10 minutes.

knowledgediscovery

Analysis code for knowledge discovery project

learn_to_code

Resources for budding developers

lolviz

A simple Python data-structure visualization tool for lists of lists, lists, dictionaries; primarily for use in Jupyter notebooks / presentations

Mask_RCNN

Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow

medic

a Python 3 command-line tool to maintain a DB mirror of MEDLINE (https://pypi.python.org/pypi/medic) - ALERT: As I have moved out of science and am working as a consultant now, this project might need a new maintainer once PubMed changes its XML format. Heroes?

nanopore-scripts

Various scripts and recipes for working with nanopore data

nbopen

Open an IPython notebook in the best available server

NCBIComputationalCookbook

Jupyter notebooks to more effectively leverage computational resources at NCBI.

NCBI_Jupyter

A variety of NCBI Computational Tools Distributed as Jupyter Notebooks

Network-Analysis-Made-Simple

For PyCon, PyData, ODSC, and beyond!

ngs-notebooks

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ngs-pipeline-ipython-notebook

Next generation sequencing pipeline python notebook

Build-a-Reproducible-Jupyter-Workflow-From-Scratch

2017 NIH Hour of Code

Build-a-Reproducible-Jupyter-Workflow-From-Scratch

2017 NIH Hour of Code

notebook

My personal and public notes.

nvariant

A python package to compute clusters of sequence feature variant types (SFVTs) based upon user-selected subsequence.

organization-RR-Jupyter

Data and project organization for Reproducible Research with the Jupyter notebook curriculum

packtSnatch

Script for ordering and downloading ebooks from packtpub freelearning page

pandas_exercises

Practice your pandas skills!

pomegranate

Graphical models for Python, implemented in Cython for speed.

poreFUME_paper

Provides Jupyter notebooks to analyse the poreFUME output

poretools

a toolkit for working with Oxford nanopore data

presentations

Bring Your Own Bioinformatics

progbio

Teaching materials for classes teaching programming to biologists

Projects

A list of practical projects that anyone can solve in any programming language.

py2cytoscape

Python utilities for Cytoscape and Cytoscape.js

pycaffe-recurrent

IPython notebook for training multilayer LSTM and RNN networks with pycaffe

pydeps

Python Module Dependency graphs

pyeq2

A very large collection of Python equations that can fit themselves to both 2D and 3D data sets, output source code in several computing languages, and run a genetic algorithm for initial parameter estimation. Comes with cluster, parallel processing and web-based graphical examples. Includes orthogonal distance and relative error regressions.

pylearn2

A Machine Learning library based on Theano

python_biologist

Python Programming for Biologists

PythonCrashCourse

A quick introduction to Python for Scientists and Engineers

PythonDataScienceHandbook

Jupyter Notebooks for the Python Data Science Handbook

python-in-a-notebook

Collection of Jupyter Notebooks about Python programming

python-jumpstart-course-demos

Contains all the "handout" materials for my Python Jumpstart by Building 10 Apps course. This includes try it yourself and finished versions of the 10 apps.

python-novice-gapminder

Introduction to Python for non-programmers using gapminder data

python-novice-inflammation

Software Carpentry introduction to Python for novices using inflammation data.

python-programming-for-biologists

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python-training-for-biologists

Python programming training for Biologists

py-viz-blog

Code for Pythonic visualization blog post

QuasiRecomb

Probabilistic inference of viral quasispecies subject to recombination (viral haplotype reconstruction).

reproducibility-guide

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resume

Python resume generator. From YAML to PDF and static HTML.

rnn-tutorial-rnnlm

Recurrent Neural Network Tutorial, Part 2 - Implementing a RNN in Python and Theano

rr-init

Research project initialization and organization following reproducible research guidelines

rr-jupyter-workshop

Overview of Jupyter RR workshop

sacred

Sacred is a tool to help you configure, organize, log and reproduce experiments developed at IDSIA.

scibot

Receive an article, parse RRIDs, resolve them, create annotations, log results

scientific_computing_2017

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scientific-python-lectures

Lectures on scientific computing with python, as IPython notebooks.

scipyUS2016_dl-image

Introduction to Deep Learning for Image Recognition - SciPy US 2016

semester-biology

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setup

Reproducible system setup

sharing-github

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sickbeard_mp4_automator

Automatically convert video files to a standardized mp4 format with proper metadata tagging to create a beautiful and uniform media library

software-vs-data

understanding and documenting the differences between software and data in the context of citation

statistical-analysis-python-tutorial

Statistical Data Analysis in Python

statlearning-notebooks

Python notebooks for exercises covered in Stanford statlearning class (where exercises were in R).

ten-rules

null

tree-tools

Various scripts for working with nested text outlines

tsri-lecture

Course material for TSRI network biology lecture

unix-for-biologists

Unix Fundamentals for Biologists

v4

Software Carpentry Version 4 lessons.

Version3.x

Version 3.x of RsyncOSX

write-ups

Write ups about computational stuff, how-tos, and explanations

xbrowse

null

yahmm

Yet Another Hidden Markov Model repository.

zika-pipeline

The Zika bioinformatics pipeline

Commits To